Download and compile the beta version of cpptraj from here:
https://github.com/Amber-MD/cpptraj
Configure like so:
./configure -amberlib -nosanderlib <compiler>
where <compiler> are the same compilers you used to compile Amber
(e.g. gnu). If you get complaints about libraries not found you can
use the '-noX' options to disable. For example if there is no bzip2
support use '-nobzlib'.
Then 'make install'. This will create the cpptraj binary in the 'bin'
subdirectory. Try using that - will be version 16.00b.
-Dan
On Wed, Mar 16, 2016 at 10:58 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com> wrote:
> **
> Cpptraj version:
> CPPTRAJ: Trajectory Analysis. V15.00
>
>
>
> On Tue, Mar 15, 2016 at 8:00 PM, <amber-request.ambermd.org> wrote:
>
>> Send AMBER mailing list submissions to
>> amber.ambermd.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://lists.ambermd.org/mailman/listinfo/amber
>> or, via email, send a message with subject or body 'help' to
>> amber-request.ambermd.org
>>
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>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of AMBER digest..."
>>
>>
>> AMBER Mailing List Digest
>>
>> Today's Topics:
>>
>> 1. Lifetime analysis of backbone hydrogen bonds
>> (Krantzman, Kristin D)
>> 2. Re: Lifetime analysis of backbone hydrogen bonds (Daniel Roe)
>> 3. Re: Lifetime analysis of backbone hydrogen bonds
>> (Krantzman, Kristin D)
>> 4. Re: Lifetime analysis of backbone hydrogen bonds
>> (Krantzman, Kristin D)
>> 5. Re: Lifetime analysis of backbone hydrogen bonds (Daniel Roe)
>> 6. Re: Problems when trying to improve angle parameters whith
>> paramfit (J?r?mie)
>> 7. Re: Problems when trying to improve angle parameters whith
>> paramfit (David Cerutti)
>> 8. Re: Problems when trying to improve angle parameters whith
>> paramfit (Robin Betz)
>> 9. Convergence problem with the SCC-DFTB example. (Jinfeng Huang)
>> 10. A query about using random seed generator in simulations
>> (anu chandra)
>> 11. Attempting MC barostat change: Failed (Michael Shokhen)
>> 12. Re: pseudo trajectories for 4 centers of mass? (Hirdesh Kumar)
>> 13. Re: A query about using random seed generator in simulations
>> (David A Case)
>> 14. Re: pseudo trajectories for 4 centers of mass? (Daniel Roe)
>> 15. Re: Attempting MC barostat change: Failed (Daniel Roe)
>> 16. Re: Attempting MC barostat change: Failed (Niel Henriksen)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 14 Mar 2016 19:28:55 +0000
>> From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu>
>> Subject: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <992A5F61E62A024D8E3580E4C42CD4853A6DB5AE.COLONIAL.COUGARS.INT>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Greetings!
>> I am using cpptraj to perform lifetime analysis of the backbond hydrogen
>> bonds in a polypeptide.
>> I am confused about some of the information produced in the output files.
>> I first execute the command:
>> hbond Backbone :1-22.C,O,N,H avgout BB.avg.dat series uuseries bbhond.gnu
>> and run.
>> Then I execute the commands:
>> lifetime Backbone[solutehb] out backbone.lifetime.dat
>> runanalysis.
>> There are 20,000 frames in my trajectory file.
>>
>> Two files are generated.
>> The first file called backbone.lifetime.dat has 60 sets, i.e. 60 hydrogen
>> bonds.
>> I am not sure what the items are in Nlifetime, MaxLT, AvgLT and
>> TotFrames. I
>> The second file called crv.backbone.lifetime.dat
>> has 26 frames with 60 curves.
>> I have read the information in the Amber15 manual, but I am still not
>> understanding exactly what the information means.
>> If you have any guidance or suggest a reference that I could read, I would
>> appreciate it.
>> Thanks in advance!
>> Best, Kristin D. Krantzman
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 14 Mar 2016 13:45:09 -0600
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAAC0qObUQm1Sr_kvkM1_V078o2Bun2OnrSGR40892UF2PRnOtA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
>> <KrantzmanK.cofc.edu> wrote:
>> > I am not sure what the items are in Nlifetime, MaxLT, AvgLT and
>> TotFrames. I
>>
>> Nlifetime is the total number of lifetimes (i.e. contiguous segments
>> of time where the hbond was "present") experienced by that hbond.
>> MaxLT is the maximum lifetime observed in frames.
>> AvgLT is the average over all lifetimes in frames.
>> TotFrames is the total number of frames over all lifetimes.
>>
>> > The second file called crv.backbone.lifetime.dat
>> > has 26 frames with 60 curves.
>> > I have read the information in the Amber15 manual, but I am still not
>> understanding exactly what the information means.
>>
>> A "lifetime curve" is essentially the curve created by adding all
>> observed lifetimes on top of each other (and normalized so that 0.0 is
>> 1.0 by default). For example, take the raw data set (this could be any
>> individual *[solutehb] series data):
>>
>> 01111000110000010011110
>>
>> Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
>> this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
>> and 4. Taken individually they look like:
>>
>> 1111
>> 11
>> 1
>> 1111
>>
>> The raw "lifetime curve" is then calculated as follows: for each frame
>> in all lifetimes up to the max lifetime (in this case 4) sum up the
>> individual lifetimes. So in this case the raw lifetime curve would
>> look like:
>>
>> 4 3 2 2
>>
>> You can read this as all four lifetimes are present at frame 1, only
>> three lifetimes are still present at frame 2, and only two lifetimes
>> are still present at frames 3 and 4. This gives you information about
>> the dynamic behavior of the lifetime (is it long-lived, does it decay
>> quickly, etc).
>>
>> Hope this helps,
>>
>> -Dan
>>
>> > If you have any guidance or suggest a reference that I could read, I
>> would appreciate it.
>> > Thanks in advance!
>> > Best, Kristin D. Krantzman
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Mon, 14 Mar 2016 20:34:30 +0000
>> From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu>
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <992A5F61E62A024D8E3580E4C42CD4853A6DB7C1.COLONIAL.COUGARS.INT>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Dear Daniel,
>> This was very helpful!
>> Therefore, if one residue has 104 frames, this means that the hydrogen
>> bond was present for ~ 104 frames. Just making sure that I understand.
>> Thanks, Kristin
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: Monday, March 14, 2016 3:45 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>>
>> On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
>> <KrantzmanK.cofc.edu> wrote:
>> > I am not sure what the items are in Nlifetime, MaxLT, AvgLT and
>> TotFrames. I
>>
>> Nlifetime is the total number of lifetimes (i.e. contiguous segments
>> of time where the hbond was "present") experienced by that hbond.
>> MaxLT is the maximum lifetime observed in frames.
>> AvgLT is the average over all lifetimes in frames.
>> TotFrames is the total number of frames over all lifetimes.
>>
>> > The second file called crv.backbone.lifetime.dat
>> > has 26 frames with 60 curves.
>> > I have read the information in the Amber15 manual, but I am still not
>> understanding exactly what the information means.
>>
>> A "lifetime curve" is essentially the curve created by adding all
>> observed lifetimes on top of each other (and normalized so that 0.0 is
>> 1.0 by default). For example, take the raw data set (this could be any
>> individual *[solutehb] series data):
>>
>> 01111000110000010011110
>>
>> Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
>> this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
>> and 4. Taken individually they look like:
>>
>> 1111
>> 11
>> 1
>> 1111
>>
>> The raw "lifetime curve" is then calculated as follows: for each frame
>> in all lifetimes up to the max lifetime (in this case 4) sum up the
>> individual lifetimes. So in this case the raw lifetime curve would
>> look like:
>>
>> 4 3 2 2
>>
>> You can read this as all four lifetimes are present at frame 1, only
>> three lifetimes are still present at frame 2, and only two lifetimes
>> are still present at frames 3 and 4. This gives you information about
>> the dynamic behavior of the lifetime (is it long-lived, does it decay
>> quickly, etc).
>>
>> Hope this helps,
>>
>> -Dan
>>
>> > If you have any guidance or suggest a reference that I could read, I
>> would appreciate it.
>> > Thanks in advance!
>> > Best, Kristin D. Krantzman
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=7nKkgKvYlPByGATtlcUvMi-58XyfR6b7Dz16EuUf_Zg&e=
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Mon, 14 Mar 2016 20:37:02 +0000
>> From: "Krantzman, Kristin D" <KrantzmanK.cofc.edu>
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <992A5F61E62A024D8E3580E4C42CD4853A6DB890.COLONIAL.COUGARS.INT>
>> Content-Type: text/plain; charset="us-ascii"
>>
>> Oops, I meant ~ 104 continuous frames.
>> ________________________________________
>> From: Krantzman, Kristin D [KrantzmanK.cofc.edu]
>> Sent: Monday, March 14, 2016 4:34 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>>
>> Dear Daniel,
>> This was very helpful!
>> Therefore, if one residue has 104 frames, this means that the hydrogen
>> bond was present for ~ 104 frames. Just making sure that I understand.
>> Thanks, Kristin
>> ________________________________________
>> From: Daniel Roe [daniel.r.roe.gmail.com]
>> Sent: Monday, March 14, 2016 3:45 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>>
>> On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
>> <KrantzmanK.cofc.edu> wrote:
>> > I am not sure what the items are in Nlifetime, MaxLT, AvgLT and
>> TotFrames. I
>>
>> Nlifetime is the total number of lifetimes (i.e. contiguous segments
>> of time where the hbond was "present") experienced by that hbond.
>> MaxLT is the maximum lifetime observed in frames.
>> AvgLT is the average over all lifetimes in frames.
>> TotFrames is the total number of frames over all lifetimes.
>>
>> > The second file called crv.backbone.lifetime.dat
>> > has 26 frames with 60 curves.
>> > I have read the information in the Amber15 manual, but I am still not
>> understanding exactly what the information means.
>>
>> A "lifetime curve" is essentially the curve created by adding all
>> observed lifetimes on top of each other (and normalized so that 0.0 is
>> 1.0 by default). For example, take the raw data set (this could be any
>> individual *[solutehb] series data):
>>
>> 01111000110000010011110
>>
>> Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
>> this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
>> and 4. Taken individually they look like:
>>
>> 1111
>> 11
>> 1
>> 1111
>>
>> The raw "lifetime curve" is then calculated as follows: for each frame
>> in all lifetimes up to the max lifetime (in this case 4) sum up the
>> individual lifetimes. So in this case the raw lifetime curve would
>> look like:
>>
>> 4 3 2 2
>>
>> You can read this as all four lifetimes are present at frame 1, only
>> three lifetimes are still present at frame 2, and only two lifetimes
>> are still present at frames 3 and 4. This gives you information about
>> the dynamic behavior of the lifetime (is it long-lived, does it decay
>> quickly, etc).
>>
>> Hope this helps,
>>
>> -Dan
>>
>> > If you have any guidance or suggest a reference that I could read, I
>> would appreciate it.
>> > Thanks in advance!
>> > Best, Kristin D. Krantzman
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=7nKkgKvYlPByGATtlcUvMi-58XyfR6b7Dz16EuUf_Zg&e=
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=x0sKYwj53vtGzkWAkYYF1ebpiCK0D5Zew638kH4wlNI&s=mGvRBaKRIA-LBhWYi2FTuJUr5SaXCDpXG6midyAzXOI&e=
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Mon, 14 Mar 2016 14:46:32 -0600
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOazkb1yO5F=QeVMj27-ycsTz0v8sh-HpefR99g_=
>> et4fw.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Yes - 104 continuous frames where a hydrogen bond is present (based on
>> the specified geometric criteria) would be a single lifetime of length
>> 104.
>>
>> -Dan
>>
>> On Mon, Mar 14, 2016 at 2:37 PM, Krantzman, Kristin D
>> <KrantzmanK.cofc.edu> wrote:
>> > Oops, I meant ~ 104 continuous frames.
>> > ________________________________________
>> > From: Krantzman, Kristin D [KrantzmanK.cofc.edu]
>> > Sent: Monday, March 14, 2016 4:34 PM
>> > To: AMBER Mailing List
>> > Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> >
>> > Dear Daniel,
>> > This was very helpful!
>> > Therefore, if one residue has 104 frames, this means that the hydrogen
>> bond was present for ~ 104 frames. Just making sure that I understand.
>> > Thanks, Kristin
>> > ________________________________________
>> > From: Daniel Roe [daniel.r.roe.gmail.com]
>> > Sent: Monday, March 14, 2016 3:45 PM
>> > To: AMBER Mailing List
>> > Subject: Re: [AMBER] Lifetime analysis of backbone hydrogen bonds
>> >
>> > On Mon, Mar 14, 2016 at 1:28 PM, Krantzman, Kristin D
>> > <KrantzmanK.cofc.edu> wrote:
>> >> I am not sure what the items are in Nlifetime, MaxLT, AvgLT and
>> TotFrames. I
>> >
>> > Nlifetime is the total number of lifetimes (i.e. contiguous segments
>> > of time where the hbond was "present") experienced by that hbond.
>> > MaxLT is the maximum lifetime observed in frames.
>> > AvgLT is the average over all lifetimes in frames.
>> > TotFrames is the total number of frames over all lifetimes.
>> >
>> >> The second file called crv.backbone.lifetime.dat
>> >> has 26 frames with 60 curves.
>> >> I have read the information in the Amber15 manual, but I am still not
>> understanding exactly what the information means.
>> >
>> > A "lifetime curve" is essentially the curve created by adding all
>> > observed lifetimes on top of each other (and normalized so that 0.0 is
>> > 1.0 by default). For example, take the raw data set (this could be any
>> > individual *[solutehb] series data):
>> >
>> > 01111000110000010011110
>> >
>> > Each contiguous segment of '1' (i.e. "present") is a lifetime, so for
>> > this set of data 4 lifetimes are observed, with lengths of 4, 2, 1,
>> > and 4. Taken individually they look like:
>> >
>> > 1111
>> > 11
>> > 1
>> > 1111
>> >
>> > The raw "lifetime curve" is then calculated as follows: for each frame
>> > in all lifetimes up to the max lifetime (in this case 4) sum up the
>> > individual lifetimes. So in this case the raw lifetime curve would
>> > look like:
>> >
>> > 4 3 2 2
>> >
>> > You can read this as all four lifetimes are present at frame 1, only
>> > three lifetimes are still present at frame 2, and only two lifetimes
>> > are still present at frames 3 and 4. This gives you information about
>> > the dynamic behavior of the lifetime (is it long-lived, does it decay
>> > quickly, etc).
>> >
>> > Hope this helps,
>> >
>> > -Dan
>> >
>> >> If you have any guidance or suggest a reference that I could read, I
>> would appreciate it.
>> >> Thanks in advance!
>> >> Best, Kristin D. Krantzman
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >>
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__home.chpc.utah.edu_-7Echeatham_&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=7nKkgKvYlPByGATtlcUvMi-58XyfR6b7Dz16EuUf_Zg&e=
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=wuSDjSHAtEcpjt79xVDv7jOiD6JtkwBZT6yxg3PRNRE&s=89Bl8cjsObIsoTQMiluwdOpilFWzn_sS-vVrSR8H1Qs&e=
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> >
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=7MSSWy9Bs2yocjNQzurxOQ&r=rDr-VDoXCKpr5ouXXYSZkHF6q5gU19w8m7W8WZccZ7U&m=x0sKYwj53vtGzkWAkYYF1ebpiCK0D5Zew638kH4wlNI&s=mGvRBaKRIA-LBhWYi2FTuJUr5SaXCDpXG6midyAzXOI&e=
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Mon, 14 Mar 2016 21:34:57 +0000
>> From: J?r?mie KNOOPS [531802] <Jeremie.KNOOPS.umons.ac.be>
>> Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> whith paramfit
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> AC59EFDB1B3AFC4EA441A07761D3E99925C18769.ExchangeMDB09.umons.ac.be>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi,
>>
>> No, I'm sorry but I do not find a solution.
>> I also thougth of using mdgx, but I didn't try yet.
>>
>> J?r?mie Knoops
>> ________________________________________
>> De : Sigurd Friis Truelsen [sigut.env.dtu.dk]
>> Envoy? : lundi 14 mars 2016 16:28
>> ? : AMBER Mailing List
>> Cc : J?r?mie KNOOPS [531802]
>> Objet : Re: [AMBER] Problems when trying to improve angle parameters
>> whith paramfit
>>
>> Dear J?r?mie and Amber Users,
>>
>> >Dear Amber Users,
>> >
>> >I'm trying to improve angle parameters but paramfit seems not able to
>> read angle parameters from the file which specify the parameters to fit.
>> >This looks like an old issue that seems to have been fixed (
>> http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
>> 15.
>> >When I specify only angle parameters, I get this message : ERROR IN MAIN
>> - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> >How to fix this bug?
>> >
>> >Thanks,
>> >
>> >J?r?mie Knoops
>>
>> I have the same problem when trying to fit angle parameters defined in a
>> file. If only angles are to be fitted I get the ERROR message like yours.
>> If I specify to fit everything in the file, Paramfit will perform the fit
>> on bonds and dihedrals, but not on the angles.
>> The only way I can get the angles to be fitted is to set
>> "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
>> this is not necessarily desired.
>> Did you find a solution for this problem?
>>
>> Best regards,
>>
>> Sigurd Truelsen
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> ------------------------------
>>
>> Message: 7
>> Date: Mon, 14 Mar 2016 18:07:10 -0400
>> From: David Cerutti <dscerutti.gmail.com>
>> Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> whith paramfit
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAEmzWj1CVs82Zo3jjq-d2WD+gexz-RABMOLQ1azOTrudumvdBg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> I am at the ACS now but I will do what I can to help you get this
>> straightened out. As long as you have an energy surface and a list of
>> parameters to target mdgx will take care of it; I talked this morning about
>> "best practices" but mdgx doesn't ask where your data came from.
>> On Mar 14, 2016 2:35 PM, "J?r?mie KNOOPS [531802]" <
>> Jeremie.KNOOPS.umons.ac.be> wrote:
>>
>> > Hi,
>> >
>> > No, I'm sorry but I do not find a solution.
>> > I also thougth of using mdgx, but I didn't try yet.
>> >
>> > J?r?mie Knoops
>> > ________________________________________
>> > De : Sigurd Friis Truelsen [sigut.env.dtu.dk]
>> > Envoy? : lundi 14 mars 2016 16:28
>> > ? : AMBER Mailing List
>> > Cc : J?r?mie KNOOPS [531802]
>> > Objet : Re: [AMBER] Problems when trying to improve angle parameters
>> > whith paramfit
>> >
>> > Dear J?r?mie and Amber Users,
>> >
>> > >Dear Amber Users,
>> > >
>> > >I'm trying to improve angle parameters but paramfit seems not able to
>> > read angle parameters from the file which specify the parameters to fit.
>> > >This looks like an old issue that seems to have been fixed (
>> > http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
>> > 15.
>> > >When I specify only angle parameters, I get this message : ERROR IN
>> MAIN
>> > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> > >How to fix this bug?
>> > >
>> > >Thanks,
>> > >
>> > >J?r?mie Knoops
>> >
>> > I have the same problem when trying to fit angle parameters defined in a
>> > file. If only angles are to be fitted I get the ERROR message like yours.
>> > If I specify to fit everything in the file, Paramfit will perform the fit
>> > on bonds and dihedrals, but not on the angles.
>> > The only way I can get the angles to be fitted is to set
>> > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
>> > this is not necessarily desired.
>> > Did you find a solution for this problem?
>> >
>> > Best regards,
>> >
>> > Sigurd Truelsen
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>> ------------------------------
>>
>> Message: 8
>> Date: Mon, 14 Mar 2016 15:38:56 -0700
>> From: Robin Betz <robin.robinbetz.com>
>> Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> whith paramfit
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAL9_cpcrzvnQ0nuVA-HS=
>> PmZxS-SFwV3XjWD7KcXx+PXqr3zvg.mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> Hi J?r?mie and Sigurd,
>>
>> So sorry! It appears there was a bug in Paramfit.
>> This should be fixed in the next version of AmberTools, but in the meantime
>> please replace file_io.c in $AMBERHOME/AmberTools/src/paramfit with the
>> attached file and recompile. The fitting should then work as expected.
>>
>> Regards,
>> Robin
>>
>>
>> On Mon, Mar 14, 2016 at 3:07 PM, David Cerutti <dscerutti.gmail.com>
>> wrote:
>>
>> > I am at the ACS now but I will do what I can to help you get this
>> > straightened out. As long as you have an energy surface and a list of
>> > parameters to target mdgx will take care of it; I talked this morning
>> about
>> > "best practices" but mdgx doesn't ask where your data came from.
>> > On Mar 14, 2016 2:35 PM, "J?r?mie KNOOPS [531802]" <
>> > Jeremie.KNOOPS.umons.ac.be> wrote:
>> >
>> > > Hi,
>> > >
>> > > No, I'm sorry but I do not find a solution.
>> > > I also thougth of using mdgx, but I didn't try yet.
>> > >
>> > > J?r?mie Knoops
>> > > ________________________________________
>> > > De : Sigurd Friis Truelsen [sigut.env.dtu.dk]
>> > > Envoy? : lundi 14 mars 2016 16:28
>> > > ? : AMBER Mailing List
>> > > Cc : J?r?mie KNOOPS [531802]
>> > > Objet : Re: [AMBER] Problems when trying to improve angle parameters
>> > > whith paramfit
>> > >
>> > > Dear J?r?mie and Amber Users,
>> > >
>> > > >Dear Amber Users,
>> > > >
>> > > >I'm trying to improve angle parameters but paramfit seems not able to
>> > > read angle parameters from the file which specify the parameters to
>> fit.
>> > > >This looks like an old issue that seems to have been fixed (
>> > > http://archive.ambermd.org/201407/0481.html) , but I'm using
>> Ambertools
>> > > 15.
>> > > >When I specify only angle parameters, I get this message : ERROR IN
>> > MAIN
>> > > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> > > >How to fix this bug?
>> > > >
>> > > >Thanks,
>> > > >
>> > > >J?r?mie Knoops
>> > >
>> > > I have the same problem when trying to fit angle parameters defined in
>> a
>> > > file. If only angles are to be fitted I get the ERROR message like
>> yours.
>> > > If I specify to fit everything in the file, Paramfit will perform the
>> fit
>> > > on bonds and dihedrals, but not on the angles.
>> > > The only way I can get the angles to be fitted is to set
>> > > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted,
>> but
>> > > this is not necessarily desired.
>> > > Did you find a solution for this problem?
>> > >
>> > > Best regards,
>> > >
>> > > Sigurd Truelsen
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: file_io.c
>> Type: text/x-csrc
>> Size: 13476 bytes
>> Desc: not available
>> Url :
>> http://lists.ambermd.org/mailman/private/amber/attachments/20160314/aaa41c67/attachment-0001.bin
>>
>> ------------------------------
>>
>> Message: 9
>> Date: Tue, 15 Mar 2016 16:29:17 +0800 (CST)
>> From: "Jinfeng Huang" <wwsshhjjff00.163.com>
>> Subject: [AMBER] Convergence problem with the SCC-DFTB example.
>> To: "amber mailist" <amber.ambermd.org>
>> Message-ID: <1b6651ae.b83d.1537964b973.Coremail.wwsshhjjff00.163.com>
>> Content-Type: text/plain; charset=GBK
>>
>> Dear all,
>> I tried to do a QM/MM simulation with amber14, but there occurs some
>> problems. I used the input file "Run.1NLN_MD_ntb1_aq1" in
>> "$AMBERHOME/test/qmmm_DFTB/1NLN_periodic_lnk_atoms_DFTB directory" and
>> corresponding prmtop and restart files. Isubmit the simulation, and errors
>> occured at the first optmize step ehich as foollows.
>>
>>
>> =================errors===============
>> QMMM SCC-DFTB: ***************************************************
>> QMMM SCC-DFTB: ERROR ON EWEVGE (Eigenvalue solver).
>> QMMM SCC-DFTB: ewevge: ier = 177 inner_scf_count= 1
>> QMMM SCC-DFTB: ***************************************************
>>
>>
>> QMMM SCC-DFTB: !!!! ============= WARNING ============= !!!!
>> QMMM SCC-DFTB: Convergence could not be achieved in this step.
>> QMMM SCC-DFTB: The calculation will continue, but energies and
>> QMMM SCC-DFTB: forces for this step will not be accurate.
>> ======================================
>>
>>
>> I confused how can I sovle the problem to continue my simulations. Any
>> help is highly appreciated!
>>
>>
>> Jinfeng
>>
>>
>> ------------------------------
>>
>> Message: 10
>> Date: Tue, 15 Mar 2016 12:14:45 +0000
>> From: anu chandra <anu80125.gmail.com>
>> Subject: [AMBER] A query about using random seed generator in
>> simulations
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CADEHHNkf4-0XLy1aH2pq+Efh+TQN-snezDpD83jcE71zSaU+EA.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Dear Amber users,
>>
>> I am using the following input parameters for doing the production run of
>> classical MD simulation with Amber.
>>
>> NVT md with random seed and netCDF output format
>> &cntrl
>> imin = 0, ntx = 5, irest = 1,
>> ntpr = 2000, ntwx = 2000, ioutfm = 1,
>> ntc = 2, ntf = 2,
>> ntt =3, gamma_ln=2.0, ig=-1,
>> nstlim = 3000000, dt =0.002,iwrap=1,
>> tempi = 300.0, temp0 = 300.0, tautp =2.0,
>> ntb = 1, ntp = 0, taup = 2.0, pres0 =1.0,
>> &end
>>
>> Following a standard protocol, I did minimization and extensive (10-20 ns)
>> equilibration of the protein-water system before entering to production
>> run. But, I am a little confused about the use random seed generator in
>> production. As per Amber manual, ig=-1 will generate different random seed
>> and thereby different staring velocity for each simulation window ( say one
>> use a 5 ns window for doing a 100 ns long simulation). Such a change in
>> velocity can bring changes in the phase space for every run ( ie, the run
>> may not be a continuation of previous window). If that the case, what is
>> the point of doing extensive equilibration here?
>>
>>
>> Many thanks
>>
>> Anu
>>
>>
>> ------------------------------
>>
>> Message: 11
>> Date: Tue, 15 Mar 2016 12:51:21 +0000
>> From: Michael Shokhen <michael.shokhen.biu.ac.il>
>> Subject: [AMBER] Attempting MC barostat change: Failed
>> To: "amber.ambermd.org" <amber.ambermd.org>
>> Message-ID:
>> <
>> DBXPR04MB01571C5738F87CB8A41FE41B6890.DBXPR04MB015.eurprd04.prod.outlook.com
>> >
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Dear Amber List experts,
>>
>>
>> I have followed all protocols from TUTORIAL A16: An Amber Lipid Force
>> Field Tutorial: Lipid14<
>> http://ambermd.org/tutorials/advanced/tutorial16/index.html>
>>
>> for MD simulation and files preparing of my protein in membrane.
>>
>> I have successfully passed all steps but the last productive MD.
>>
>> I have used prod.in file that is a copy of the original 05_Prod.in<
>> http://ambermd.org/tutorials/advanced/tutorial16/include/05_Prod.in>
>> script in the command:
>>
>> nohup pmemd.cuda -O -i prod.in<http://prod.in> -o prod1.out -p
>> ../*.prmtop \
>> -c ../4_/hold10.rst -r prod1.rst -x prod1.nc<http://prod1.nc> &
>>
>> Examining the MD output file I have observed an error message:
>>
>>
>> Attempting MC barostat change: Failed
>>
>>
>> Please find below a fragment of the output file with all details
>>
>> including the text of the used prod.in file.
>>
>>
>> Please advise me what changes in the prod.in parameters
>>
>> should be used to resolve the problem.
>>
>>
>> Thank you,
>>
>> Michael
>>
>>
>>
>> -------------------------------------------------------
>> Amber 14 SANDER 2014
>> -------------------------------------------------------
>>
>> | PMEMD implementation of SANDER, Release 14
>>
>> | Run on 03/15/2016 at 13:47:45
>>
>> | Executable path: pmemd.cuda
>> | Working directory: /home/shokhen/Documents/5f5b/5_
>> | Hostname: Unknown
>> [-O]verwriting output
>>
>> File Assignments:
>> | MDIN: prod.in
>> | MDOUT: prod1.out
>> | INPCRD: ../4_/hold10.rst
>> | PARM: ../mc.prmtop
>> | RESTRT: prod1.rst
>> | REFC: refc
>> | MDVEL: mdvel
>> | MDEN: mden
>> | MDCRD: prod1.nc
>> | MDINFO: mdinfo
>> | MDFRC: mdfrc
>>
>>
>> Here is the input file:
>>
>> Protein Lipid production 310K 125ns
>> &cntrl
>> imin=0,
>> ntx=5,
>> irest=1,
>> ntc=2,
>> ntf=2,
>> tol=0.0000001,
>> nstlim=62500000,
>> ntt=3,
>> gamma_ln=1.0,
>> temp0=303.0,
>> ntpr=5000,
>> ntwr=500000,
>> ntwx=5000,
>> dt=0.002,
>> ig=-1,
>> ntb=2,
>> ntp=2,
>> cut=10.0,
>> ioutfm=1,
>> ntxo=2,
>> barostat=2,
>> /
>>
>>
>>
>>
>>
>> Note: ig = -1. Setting random seed to 703795 based on wallclock time in
>> microseconds.
>>
>> |--------------------- INFORMATION ----------------------
>> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> | Version 14.0.1
>> |
>> | 06/20/2014
>> |
>> | Implementation by:
>> | Ross C. Walker (SDSC)
>> | Scott Le Grand (nVIDIA)
>> |
>> | CAUTION: The CUDA code is currently experimental.
>> | You use it at your own risk. Be sure to
>> | check ALL results carefully.
>> |
>> | Precision model in use:
>> | [SPFP] - Mixed Single/Double/Fixed Point Precision.
>> | (Default)
>> |
>> |--------------------------------------------------------
>>
>>
>> |------------------- GPU DEVICE INFO --------------------
>> |
>> | CUDA_VISIBLE_DEVICES: not set
>> | CUDA Capable Devices Detected: 2
>> | CUDA Device ID in use: 0
>> | CUDA Device Name: GeForce GTX TITAN
>> | CUDA Device Global Mem Size: 6143 MB
>> | CUDA Device Num Multiprocessors: 14
>> | CUDA Device Core Freq: 0.88 GHz
>> |
>> |--------------------------------------------------------
>>
>>
>> | Conditional Compilation Defines Used:
>> | PUBFFT
>> | BINTRAJ
>> | CUDA
>> | EMIL
>>
>> | Largest sphere to fit in unit cell has radius = 34.888
>>
>> | New format PARM file being parsed.
>> | Version = 1.000 Date = 03/14/16 Time = 13:03:58
>>
>> | Note: 1-4 EEL scale factors are being read from the topology file.
>>
>> | Note: 1-4 VDW scale factors are being read from the topology file.
>> | Duplicated 0 dihedrals
>>
>> | Duplicated 0 dihedrals
>>
>>
>> --------------------------------------------------------------------------------
>> 1. RESOURCE USE:
>>
>> --------------------------------------------------------------------------------
>>
>> getting box info from netcdf restart file
>> NATOM = 48860 NTYPES = 24 NBONH = 39447 MBONA = 9250
>> NTHETH = 33060 MTHETA = 10615 NPHIH = 53704 MPHIA = 35939
>> NHPARM = 0 NPARM = 0 NNB = 162244 NRES = 9308
>> NBONA = 9250 NTHETA = 10615 NPHIA = 35939 NUMBND = 88
>> NUMANG = 194 NPTRA = 253 NATYP = 53 NPHB = 1
>> IFBOX = 1 NMXRS = 50 IFCAP = 0 NEXTRA = 0
>> NCOPY = 0
>>
>> | Coordinate Index Table dimensions: 14 12 15
>> | Direct force subcell size = 5.5488 5.8147 5.8347
>>
>> BOX TYPE: RECTILINEAR
>>
>>
>> --------------------------------------------------------------------------------
>> 2. CONTROL DATA FOR THE RUN
>>
>> --------------------------------------------------------------------------------
>>
>> default_name
>>
>> General flags:
>> imin = 0, nmropt = 0
>>
>> Nature and format of input:
>> ntx = 5, irest = 1, ntrx = 1
>>
>> Nature and format of output:
>> ntxo = 2, ntpr = 5000, ntrx = 1, ntwr =
>> 500000
>> iwrap = 0, ntwx = 5000, ntwv = 0, ntwe =
>> 0
>> ioutfm = 1, ntwprt = 0, idecomp = 0, rbornstat=
>> 0
>>
>> Potential function:
>> ntf = 2, ntb = 2, igb = 0, nsnb =
>> 25
>> ipol = 0, gbsa = 0, iesp = 0
>> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>>
>> Frozen or restrained atoms:
>> ibelly = 0, ntr = 0
>>
>> Molecular dynamics:
>> nstlim = 62500000, nscm = 1000, nrespa = 1
>> t = 0.00000, dt = 0.00200, vlimit = -1.00000
>>
>> Langevin dynamics temperature regulation:
>> ig = 703795
>> temp0 = 303.00000, tempi = 0.00000, gamma_ln= 1.00000
>>
>> Pressure regulation:
>> ntp = 2
>> pres0 = 1.00000, comp = 44.60000, taup = 1.00000
>> Monte-Carlo Barostat:
>> mcbarint = 100
>>
>> SHAKE:
>> ntc = 2, jfastw = 0
>> tol = 0.00000
>>
>> | Intermolecular bonds treatment:
>> | no_intermolecular_bonds = 1
>>
>> | Energy averages sample interval:
>> | ene_avg_sampling = 5000
>>
>> Ewald parameters:
>> verbose = 0, ew_type = 0, nbflag = 1, use_pme =
>> 1
>> vdwmeth = 1, eedmeth = 1, netfrc = 1
>> Box X = 77.683 Box Y = 69.776 Box Z = 87.521
>> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>> NFFT1 = 80 NFFT2 = 72 NFFT3 = 96
>> Cutoff= 10.000 Tol =0.100E-04
>> Ewald Coefficient = 0.27511
>> Interpolation order = 4
>>
>>
>> --------------------------------------------------------------------------------
>> 3. ATOMIC COORDINATES AND VELOCITIES
>>
>> --------------------------------------------------------------------------------
>>
>> default_name
>> begin time read from input coords = 5420.000 ps
>>
>>
>> Number of triangulated 3-point waters found: 8585
>>
>> Sum of charges from parm topology file = -0.00048135
>> Forcing neutrality...
>>
>> | Dynamic Memory, Types Used:
>> | Reals 1953878
>> | Integers 3235415
>>
>> | Nonbonded Pairs Initial Allocation: 14778928
>>
>> | GPU memory information (estimate):
>> | KB of GPU memory in use: 327439
>> | KB of CPU memory in use: 69715
>>
>>
>> --------------------------------------------------------------------------------
>> 4. RESULTS
>>
>> --------------------------------------------------------------------------------
>>
>> ---------------------------------------------------
>> APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>> using 5000.0 points per unit in tabled values
>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>> ---------------------------------------------------
>> |---------------------------------------------------
>> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>> | with 50.0 points per unit in tabled values
>> | Relative Error Limit not exceeded for r .gt. 2.33
>> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>> | with 50.0 points per unit in tabled values
>> | Relative Error Limit not exceeded for r .gt. 2.80
>> |---------------------------------------------------
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | MC Barostat: Decreasing size of volume moves
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | MC Barostat: Decreasing size of volume moves
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Succeeded
>> | Attempting MC barostat change: Failed
>> | MC Barostat: Decreasing size of volume moves
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Succeeded
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | MC Barostat: Decreasing size of volume moves
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Failed
>> | Attempting MC barostat change: Succeeded
>> | Attempting MC barostat change: Failed
>> | MC Barostat: Decreasing size of volume moves
>>
>> NSTEP = 5000 TIME(PS) = 5430.000 TEMP(K) = 302.62 PRESS =
>> 0.0
>> Etot = -76479.2165 EKtot = 32212.5273 EPtot =
>> -108691.7438
>> BOND = 3129.9050 ANGLE = 12010.4285 DIHED =
>> 8922.3943
>> 1-4 NB = 3003.3686 1-4 EEL = 19841.7423 VDWAALS =
>> 2219.1152
>> EELEC = -157818.6978 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
>> 473431.6153
>> Density =
>> 1.0263
>>
>> ------------------------------------------------------------------------------
>>
>>
>> <
>> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
>> >
>>
>>
>> <
>> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
>> >
>>
>>
>> ------------------------------
>>
>> Message: 12
>> Date: Tue, 15 Mar 2016 13:54:46 +0100
>> From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
>> Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAPKknGouoOSQQKSUA79w1zAbFoR33uZvAYCaqJdqPUyrexXfAg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Thank you very much Dan!
>>
>> As per your suggestion, I tried as follows:
>>
>> vector S1 center :1-27,65-139.CA,C,N,O
>> vector S2 center :28-33,46-64.CA,C,N,O
>> vector S3 center :140-175,265-332.CA,C,N,O
>> vector S4 center :176-264.CA,C,N,O
>> create vector_traj.nc S1 S2 S3 S4 vectraj trajfmt netcdf parmout
>> vector_traj.parm7 noorigin
>>
>>
>> I was expecting a pseuto-trajectory with four atoms (and one origin) but I
>> still get a single atom.
>>
>> Thanks,
>> Hirdesh
>>
>> On Mon, Mar 14, 2016 at 8:00 PM, <amber-request.ambermd.org> wrote:
>>
>> > Send AMBER mailing list submissions to
>> > amber.ambermd.org
>> >
>> > To subscribe or unsubscribe via the World Wide Web, visit
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> > or, via email, send a message with subject or body 'help' to
>> > amber-request.ambermd.org
>> >
>> > You can reach the person managing the list at
>> > amber-owner.ambermd.org
>> >
>> > When replying, please edit your Subject line so it is more specific
>> > than "Re: Contents of AMBER digest..."
>> >
>> >
>> > AMBER Mailing List Digest
>> >
>> > Today's Topics:
>> >
>> > 1. Re: pseudo trajectories for 4 centers of mass? (Daniel Roe)
>> > 2. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> > (inp=2 in &pb namelist) (Stefan Ivanov)
>> > 3. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> > (inp=2 in &pb namelist) (Ray Luo)
>> > 4. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> > (inp=2 in &pb namelist) (Stefan Ivanov)
>> > 5. ISQBP 2016 meeting - registration opened! (Thomas Cheatham)
>> > 6. Re: AMBER:neutralisation of non integral charges (Shilpa Gupta)
>> > 7. Re: AMBER:neutralisation of non integral charges (Hannes Loeffler)
>> > 8. bad atom type with MMPBSA decomposition? (Kenneth Huang)
>> > 9. Re: Problems when trying to improve angle parameters whith
>> > paramfit (Sigurd Friis Truelsen)
>> > 10. Re: Problems when trying to improve angle parameters whith
>> > paramfit (David Cerutti)
>> > 11. parmed -setBond command (Balaji Selvam)
>> > 12. Re: parmed -setBond command (Daniel Roe)
>> >
>> >
>> > ----------------------------------------------------------------------
>> >
>> > Message: 1
>> > Date: Sun, 13 Mar 2016 14:40:39 -0600
>> > From: Daniel Roe <daniel.r.roe.gmail.com>
>> > Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <
>> > CAAC0qOavS0Upk9-A9TbFKpo7t36+pqpX_VLga-0FeA3DL8pReg.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Hi,
>> >
>> > On Sun, Mar 13, 2016 at 11:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
>> > wrote:
>> > >
>> > > It would be great if I can visualize four center of masses as a
>> "single"
>> > > molecule in VMD.
>> >
>> > You can do this by writing your vector data as a pseudo trajectory via
>> > 'vectraj', e.g.
>> >
>> > parm myparm.parm7
>> > trajin mytraj.nc
>> > vector V1 center <mask1>
>> > vector V2 center <mask2>
>> > vector V3 center <mask3>
>> > vector V4 center <mask4>
>> > create vector_traj.nc V1 V2 V3 V4 vectraj trajfmt netcdf \
>> > parmout vector_traj.parm7 noorigin
>> >
>> > This will create a pseudo trajectory containing your vector data. To
>> > ensure that this script works as-is you should use the GitHub beta
>> > version of cpptraj. If you want to use the AmberTools version of
>> > cpptraj do not include the 'noorigin' keyword since that is not yet
>> > implemented in that version.
>> >
>> > Hope this helps,
>> >
>> > -Dan
>> >
>> > >
>> > > Thanks,
>> > > Hirdesh
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Mon, 14 Mar 2016 02:11:01 +0000
>> > From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
>> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> > 14? (inp=2 in &pb namelist)
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <58F9FB3DCABE5F4F905560AB46873D7C77320B04.MBXP05.ds.man.ac.uk>
>> > Content-Type: text/plain; charset="iso-8859-7"
>> >
>> > Hi Prof Luo,
>> >
>> > Thank you very much for your helpful and informative reply.
>> >
>> > If I understand correctly, by default:
>> >
>> > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension and
>> c
>> > is the cavity offset, correct? How is the volume computed? More
>> precisely,
>> > what volume is being used - solvent accessible (SAV) or solvent excluded
>> > volume (SEV)?
>> >
>> > As for the keywords in the output:
>> >
>> >
>> > EPB = ?Gelectrostatic
>> > ENPOLAR = ?Gattractive (?Gdispersion)
>> > ECAVITY = ?Grepulsive(?Gcavitation)
>> >
>> > and
>> >
>> > ?Gnonpolar = ENPOLAR + ECAVITY
>> >
>> > Finally,
>> >
>> > ?Gsolvation = ?Gnonpolar + EPB
>> >
>> > Is this correct?
>> >
>> > Best wishes,
>> >
>> > Stefan
>> >
>> >
>> > ________________________________________
>> > From: Ray Luo [rluo.uci.edu]
>> > Sent: Sunday, March 13, 2016 4:21 AM
>> > To: AMBER Mailing List
>> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> > 14? (inp=2 in &pb namelist)
>> >
>> > Hi Stefan,
>> >
>> > > I would like to ask a few questions regarding MMPBSA.py's
>> > > implementation in AMBER14. Having read the AMBER14 manual, the
>> > > MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> > > bit confused and unsure about a few things.
>> > >
>> > > What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> > > in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> > > I'm specifically talking about the Poisson-Boltzmann computations, i.e.
>> > > inp=2 in the &pb namelist (which is equivalent to not specifying
>> > > anything for inp, because 2 is the default value, right)?. I think the
>> > > manual is a bit unclear. From what I understand
>> >
>> > This is correct.
>> >
>> > > ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> > >
>> > > and
>> > >
>> > > ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> >
>> > Yes, this is correct.
>> >
>> > > Finally:
>> > >
>> > > ?Grepulsive = ?*SASA + c
>> >
>> > The default behavior is that the repulsive free energy is modeled as
>> > linearly depended on the volume within SASA since this is the best
>> > observed scheme for the tested small molecules and side chain mutation
>> > data.
>> >
>> > > where SASA is computed with the LCPO method. Is this correct or is
>> > > the cavitation term proportional to molecular volume? If so, how is
>> that
>> > > computed?
>> >
>> > If you choose to model it as linearly dependent on SASA, PBSA would
>> > compute SASA numerically, it does not use the approximated LCPO
>> > method.
>> >
>> > > Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> > > EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> > > the (repulsive) cavitation term and EDISPER is the (attractive)
>> > > dispersion term (although in this case ENPOLAR is negative and
>> > > ECAVITY is positive)?
>> >
>> > This is because the the printing of ECAVITY (inp=2) shares the same
>> > routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> > because they both use linearly functional models. The sander printout
>> > is more informative.
>> >
>> > > Also, is the internal PBSA solver in sander linear or nonlinear?
>> >
>> > It's linear by default.
>> >
>> > > I have seen a lot of recommendations for the "perl" version of
>> > > MMPBSA, but very little for MMPBSA.py. What settings would you
>> > > recommend for doing Poisson-Boltzmann calculations on protein -
>> > > protein complexes?
>> >
>> > The two scripts should give you the same results if you use the same
>> > options. The difference is that the perl script uses sander, and the
>> > python script uses nab by default. If you prefer, you can use the
>> > sander option in the python script so you can choose all the &pb
>> > keywords as described in the manual. Apparently it is too hard to
>> > support all &pb keywords in either scripts.
>> >
>> > You may want to use inp=1 for protein-protein complexes because the
>> > inp=2 was not optimized for macromolecular "ligand" binding, though we
>> > are working on it.
>> >
>> > All the best,
>> > Ray
>> > --
>> > Ray Luo, Ph.D.
>> > Professor
>> > Biochemistry, Molecular Biophysics, Chemical Physics,
>> > Chemical and Biomedical Engineering
>> > University of California, Irvine, CA 92697-3900
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 3
>> > Date: Sun, 13 Mar 2016 20:52:30 -0700
>> > From: Ray Luo <rluo.uci.edu>
>> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> > 14? (inp=2 in &pb namelist)
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <
>> > CAOg1T6Sev165TLOpeGutcdgD4ZWnufx7Q1eYgDsx0VZCbzEyPA.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Hi Stefan,
>> >
>> > > If I understand correctly, by default:
>> > >
>> > > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension
>> and
>> > c is the cavity offset, correct? How is the volume computed? More
>> > precisely, what volume is being used - solvent accessible (SAV) or
>> solvent
>> > excluded volume (SEV)?
>> >
>> > Yes, and it uses SAV since it performs better as shown in the original
>> > paper.
>> >
>> > > As for the keywords in the output:
>> > >
>> > > EPB = ?Gelectrostatic
>> > > ENPOLAR = ?Gattractive (?Gdispersion)
>> > > ECAVITY = ?Grepulsive(?Gcavitation)
>> >
>> > In the python script (please refer to your own output):
>> >
>> > ENPOLAR is the repulsive free energy; it's positive.
>> > EDISPER is the attractive free energy; it's negative.
>> >
>> > > and
>> > >
>> > > ?Gnonpolar = ENPOLAR + ECAVITY
>> >
>> > Yes.
>> >
>> > > Finally,
>> > >
>> > > ?Gsolvation = ?Gnonpolar + EPB
>> > >
>> > > Is this correct?
>> >
>> > Yes.
>> >
>> > All the best,
>> > Ray
>> > --
>> > Ray Luo, Ph.D.
>> > Professor
>> > Biochemistry, Molecular Biophysics, Chemical Physics,
>> > Chemical and Biomedical Engineering
>> > University of California, Irvine, CA 92697-3900
>> >
>> > > ________________________________________
>> > > From: Ray Luo [rluo.uci.edu]
>> > > Sent: Sunday, March 13, 2016 4:21 AM
>> > > To: AMBER Mailing List
>> > > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in
>> AMBER
>> > 14? (inp=2 in &pb namelist)
>> > >
>> > > Hi Stefan,
>> > >
>> > >> I would like to ask a few questions regarding MMPBSA.py's
>> > >> implementation in AMBER14. Having read the AMBER14 manual, the
>> > >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> > >> bit confused and unsure about a few things.
>> > >>
>> > >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> > >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> > >> I'm specifically talking about the Poisson-Boltzmann computations,
>> i.e.
>> > >> inp=2 in the &pb namelist (which is equivalent to not specifying
>> > >> anything for inp, because 2 is the default value, right)?. I think the
>> > >> manual is a bit unclear. From what I understand
>> > >
>> > > This is correct.
>> > >
>> > >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> > >>
>> > >> and
>> > >>
>> > >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> > >
>> > > Yes, this is correct.
>> > >
>> > >> Finally:
>> > >>
>> > >> ?Grepulsive = ?*SASA + c
>> > >
>> > > The default behavior is that the repulsive free energy is modeled as
>> > > linearly depended on the volume within SASA since this is the best
>> > > observed scheme for the tested small molecules and side chain mutation
>> > > data.
>> > >
>> > >> where SASA is computed with the LCPO method. Is this correct or is
>> > >> the cavitation term proportional to molecular volume? If so, how is
>> that
>> > >> computed?
>> > >
>> > > If you choose to model it as linearly dependent on SASA, PBSA would
>> > > compute SASA numerically, it does not use the approximated LCPO
>> > > method.
>> > >
>> > >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> > >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> > >> the (repulsive) cavitation term and EDISPER is the (attractive)
>> > >> dispersion term (although in this case ENPOLAR is negative and
>> > >> ECAVITY is positive)?
>> > >
>> > > This is because the the printing of ECAVITY (inp=2) shares the same
>> > > routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> > > because they both use linearly functional models. The sander printout
>> > > is more informative.
>> > >
>> > >> Also, is the internal PBSA solver in sander linear or nonlinear?
>> > >
>> > > It's linear by default.
>> > >
>> > >> I have seen a lot of recommendations for the "perl" version of
>> > >> MMPBSA, but very little for MMPBSA.py. What settings would you
>> > >> recommend for doing Poisson-Boltzmann calculations on protein -
>> > >> protein complexes?
>> > >
>> > > The two scripts should give you the same results if you use the same
>> > > options. The difference is that the perl script uses sander, and the
>> > > python script uses nab by default. If you prefer, you can use the
>> > > sander option in the python script so you can choose all the &pb
>> > > keywords as described in the manual. Apparently it is too hard to
>> > > support all &pb keywords in either scripts.
>> > >
>> > > You may want to use inp=1 for protein-protein complexes because the
>> > > inp=2 was not optimized for macromolecular "ligand" binding, though we
>> > > are working on it.
>> > >
>> > > All the best,
>> > > Ray
>> > > --
>> > > Ray Luo, Ph.D.
>> > > Professor
>> > > Biochemistry, Molecular Biophysics, Chemical Physics,
>> > > Chemical and Biomedical Engineering
>> > > University of California, Irvine, CA 92697-3900
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 4
>> > Date: Mon, 14 Mar 2016 05:11:33 +0000
>> > From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
>> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> > 14? (inp=2 in &pb namelist)
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <58F9FB3DCABE5F4F905560AB46873D7C77320B19.MBXP05.ds.man.ac.uk>
>> > Content-Type: text/plain; charset="iso-8859-7"
>> >
>> > Hi Prof Luo,
>> >
>> > Many thanks and best wishes,
>> >
>> > Stefan
>> >
>> >
>> > ________________________________________
>> > From: Ray Luo [rluo.uci.edu]
>> > Sent: Monday, March 14, 2016 3:52 AM
>> > To: AMBER Mailing List
>> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> > 14? (inp=2 in &pb namelist)
>> >
>> > Hi Stefan,
>> >
>> > > If I understand correctly, by default:
>> > >
>> > > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension
>> and
>> > c is the cavity offset, correct? How is the volume computed? More
>> > precisely, what volume is being used - solvent accessible (SAV) or
>> solvent
>> > excluded volume (SEV)?
>> >
>> > Yes, and it uses SAV since it performs better as shown in the original
>> > paper.
>> >
>> > > As for the keywords in the output:
>> > >
>> > > EPB = ?Gelectrostatic
>> > > ENPOLAR = ?Gattractive (?Gdispersion)
>> > > ECAVITY = ?Grepulsive(?Gcavitation)
>> >
>> > In the python script (please refer to your own output):
>> >
>> > ENPOLAR is the repulsive free energy; it's positive.
>> > EDISPER is the attractive free energy; it's negative.
>> >
>> > > and
>> > >
>> > > ?Gnonpolar = ENPOLAR + ECAVITY
>> >
>> > Yes.
>> >
>> > > Finally,
>> > >
>> > > ?Gsolvation = ?Gnonpolar + EPB
>> > >
>> > > Is this correct?
>> >
>> > Yes.
>> >
>> > All the best,
>> > Ray
>> > --
>> > Ray Luo, Ph.D.
>> > Professor
>> > Biochemistry, Molecular Biophysics, Chemical Physics,
>> > Chemical and Biomedical Engineering
>> > University of California, Irvine, CA 92697-3900
>> >
>> > > ________________________________________
>> > > From: Ray Luo [rluo.uci.edu]
>> > > Sent: Sunday, March 13, 2016 4:21 AM
>> > > To: AMBER Mailing List
>> > > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in
>> AMBER
>> > 14? (inp=2 in &pb namelist)
>> > >
>> > > Hi Stefan,
>> > >
>> > >> I would like to ask a few questions regarding MMPBSA.py's
>> > >> implementation in AMBER14. Having read the AMBER14 manual, the
>> > >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> > >> bit confused and unsure about a few things.
>> > >>
>> > >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> > >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> > >> I'm specifically talking about the Poisson-Boltzmann computations,
>> i.e.
>> > >> inp=2 in the &pb namelist (which is equivalent to not specifying
>> > >> anything for inp, because 2 is the default value, right)?. I think the
>> > >> manual is a bit unclear. From what I understand
>> > >
>> > > This is correct.
>> > >
>> > >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> > >>
>> > >> and
>> > >>
>> > >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> > >
>> > > Yes, this is correct.
>> > >
>> > >> Finally:
>> > >>
>> > >> ?Grepulsive = ?*SASA + c
>> > >
>> > > The default behavior is that the repulsive free energy is modeled as
>> > > linearly depended on the volume within SASA since this is the best
>> > > observed scheme for the tested small molecules and side chain mutation
>> > > data.
>> > >
>> > >> where SASA is computed with the LCPO method. Is this correct or is
>> > >> the cavitation term proportional to molecular volume? If so, how is
>> that
>> > >> computed?
>> > >
>> > > If you choose to model it as linearly dependent on SASA, PBSA would
>> > > compute SASA numerically, it does not use the approximated LCPO
>> > > method.
>> > >
>> > >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> > >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> > >> the (repulsive) cavitation term and EDISPER is the (attractive)
>> > >> dispersion term (although in this case ENPOLAR is negative and
>> > >> ECAVITY is positive)?
>> > >
>> > > This is because the the printing of ECAVITY (inp=2) shares the same
>> > > routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> > > because they both use linearly functional models. The sander printout
>> > > is more informative.
>> > >
>> > >> Also, is the internal PBSA solver in sander linear or nonlinear?
>> > >
>> > > It's linear by default.
>> > >
>> > >> I have seen a lot of recommendations for the "perl" version of
>> > >> MMPBSA, but very little for MMPBSA.py. What settings would you
>> > >> recommend for doing Poisson-Boltzmann calculations on protein -
>> > >> protein complexes?
>> > >
>> > > The two scripts should give you the same results if you use the same
>> > > options. The difference is that the perl script uses sander, and the
>> > > python script uses nab by default. If you prefer, you can use the
>> > > sander option in the python script so you can choose all the &pb
>> > > keywords as described in the manual. Apparently it is too hard to
>> > > support all &pb keywords in either scripts.
>> > >
>> > > You may want to use inp=1 for protein-protein complexes because the
>> > > inp=2 was not optimized for macromolecular "ligand" binding, though we
>> > > are working on it.
>> > >
>> > > All the best,
>> > > Ray
>> > > --
>> > > Ray Luo, Ph.D.
>> > > Professor
>> > > Biochemistry, Molecular Biophysics, Chemical Physics,
>> > > Chemical and Biomedical Engineering
>> > > University of California, Irvine, CA 92697-3900
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 5
>> > Date: Sun, 13 Mar 2016 23:15:46 -0600 (MDT)
>> > From: Thomas Cheatham <tec3.utah.edu>
>> > Subject: [AMBER] ISQBP 2016 meeting - registration opened!
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <alpine.OSX.2.20.1603132314110.7776.thomass-macbook-air-3.local>
>> > Content-Type: text/plain; charset="iso-8859-15"
>> >
>> >
>> > ...opportunities for people to speak! --tec3
>> >
>> >
>> > Dear colleagues,?
>> >
>> > We are thrilled to announce that the registration for the President's
>> > Meeting 2016 of the International Society of Quantum Biology and
>> > Pharmacology (ISQBP) is now opened!?
>> >
>> > The program will feature oral presentations by an exciting line up of
>> > invited speakers (see list below). In addition we welcome abstract
>> > submission for ca. 15 short oral presentations and ?posters, with a focus
>> > on the following topics: nucleic acids, enzyme catalysis, protein-lipid
>> > interactions, methods development, protein dynamics and drug design.?
>> >
>> > Registration and abstract submission forms can be found
>> > at?www.isqbp2016.org.
>> >
>> > DATE: 19-22 June 2016?
>> >
>> > PLACE: Grand Hotel Terminus, Bergen, Norway (www.grandterminus.no/en/).
>> > The venue is conveniently located in the city center of Bergen, with
>> > frequent transfer from the airport (30 minutes drive by airport bus or
>> > taxi).
>> >
>> > INVITED SPEAKERS: Charles L. Brooks III, Thomas E. Cheatham III, Vlad
>> > Cojoracu, Annick Dejaegere, Carmen Domene, William L. Jorgensen, Syma
>> > Khalid, Carmay Lim, Alex MacKerell, Lennart Nilsson, Masha Niv, Modesto
>> > Orozco, Montgomery Pettitt, Carol Post, Rebecca Wade
>> >
>> > ABSTRACTS: we are welcoming abstracts for ca. 15 short oral presentations
>> > and posters.
>> >
>> > IMPORTANT DATES:
>> > Early bird registration until March 20th
>> > Abstract submission deadline for talks: March 20th
>> > Abstract submission deadline for posters: April 15th
>> >
>> > TRAVEL AWARDS: Two ISQBP travel awards will be provided by the Society to
>> > support students presenting their work at the meeting. The selection will
>> > be based on the creativity, relevance and quality of the work as well as
>> > the distance the student has to travel to attend the conference.
>> >
>> > MEETING WEBSITE:?www.isqbp2016.org
>> >
>> > ISQBP: want to know more about the International Society of Quantum
>> > Biology and Pharmacology? Visit our webpage at?
>> http://isqbp.umaryland.edu
>> >
>> >
>> >
>> >
>> > With best regards,
>> > The Scientific Committee
>> >
>> > Nathalie Reuter?
>> > (Computational Biology Unit, University of Bergen)
>> >
>> > Bjorn Olav Brandsdal?
>> > (Centre for Theoretical and Computational Chemistry, University of
>> Tromso)
>> >
>> > Michele Cascella
>> > (Centre for Theoretical and Computational Chemistry, University of
>> Oslo)To
>> > join or leave the
>> > molecular-dynamics-news email list, go to:
>> > http://www.jiscmail.ac.uk/lists/molecular-dynamics-news.html
>> >
>> > ------------------------------
>> >
>> > Message: 6
>> > Date: Mon, 14 Mar 2016 13:22:42 +0000 (UTC)
>> > From: Shilpa Gupta <guptashilpa_91.yahoo.com>
>> > Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
>> > To: <amber.ambermd.org>
>> > Message-ID:
>> > <2032101966.923925.1457961762365.JavaMail.yahoo.mail.yahoo.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Dear Amber users,
>> > i am getting non integral charges (19.994) on my macromolecule. How
>> > can i neutralise the charge using addions in tleap. Thanks in advance.
>> >
>> >
>> > Shilpa Gupta
>> > University of Delhi
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 7
>> > Date: Mon, 14 Mar 2016 13:37:42 +0000
>> > From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
>> > Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
>> > To: <amber.ambermd.org>
>> > Cc: Shilpa Gupta <guptashilpa_91.yahoo.com>
>> > Message-ID: <20160314133742.6d9c6ecb.zgb83773vig.dl.ac.uk>
>> > Content-Type: text/plain; charset="US-ASCII"
>> >
>> > On Mon, 14 Mar 2016 13:22:42 +0000
>> > Shilpa Gupta <guptashilpa_91.yahoo.com> wrote:
>> >
>> > > Dear Amber users,
>> > > i am getting non integral charges (19.994) on my macromolecule.
>> > > How can i neutralise the charge using addions in tleap. Thanks in
>> > > advance.
>> >
>> > Type 'help addions' in leap and read the manual. I spotted an example
>> > in the latter when I searched for 'neutralize'.
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 8
>> > Date: Mon, 14 Mar 2016 09:58:25 -0400
>> > From: Kenneth Huang <kennethneltharion.gmail.com>
>> > Subject: [AMBER] bad atom type with MMPBSA decomposition?
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <
>> > CALeh7kBZ2duQo0Eg2y2W0q_-rj-NBXufVcgSA3eAgk14NrcTjA.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Hi all,
>> >
>> > As the subject says, I'm running into a bad atom type error with MMPBSA.
>> > Specifically when I try to run decomposition- without decomposition, it
>> > runs without any errors, but when I try to run decomp it exits after
>> > initializing with the bad atom type error.
>> >
>> > I already had two modifications in mdread2.F90 which I thought would've
>> > fixed the issue-
>> >
>> > ! Begin modifications
>> > > else if (atype == 'K+') then
>> > > x(l165-1+i) = 1.52d0 + 1.4d0
>> > > x(l170-1+i) = 0.68563d0
>> > > x(l175-1+i) = -0.1868d0
>> > > x(l180-1+i) = -0.00135573d0
>> > > x(l185-1+i) = 0.00023743d0
>> > > ! End modifications
>> > >
>> >
>> >
>> > else if (atomicnumber .eq. 12) then
>> > > ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys.
>> > > 1997, 107, 5422
>> > > ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys.
>> > > 1997, 107, 5422
>> > > ! Mg radius = 1.45A: Aqvist 1992
>> > > x(L165-1+i) = 1.18d0 + 1.4d0
>> > > ! Begin modifications
>> > > else if (atomicnumber .eq. 19) then
>> > > x(L165-1+i) = 1.52d0 + 1.4d0
>> > > ! End modifications
>> > > else
>> > > write( 0,* ) 'bad atom type: ',atype,' cannot perform
>> > >
>> >
>> > And I've double checked %FLAG ATOMIC_NUMBER in the topology files to make
>> > sure that the atomic number is correct (19), did a fresh install and
>> > recompiled in serial and parallel with the changes to mdread2.f90, but
>> I'm
>> > still getting the same error with my input as-
>> >
>> > &general
>> > endframe=1000, interval=100, keep_files=2, verbose=1,
>> > receptor_mask=':1-1044', ligand_mask=':1045-2088'
>> > /
>> > &gb
>> > igb=2, saltcon=0.100,
>> > /
>> > &pb
>> > istrng=0.100, indi=2.0, radiopt=0, inp=1,
>> > /
>> > &decomp
>> > idecomp=1, print_res="12-24; 291-308; 330-342; 365-389"
>> > dec_verbose=3,
>> > /
>> >
>> > At this point, I'm kind of baffled as to why it'd throwing up the error
>> > message since I can't find a discernible reason why it'd be tossing out
>> > that message.
>> >
>> > Best,
>> >
>> > Kenneth
>> > --
>> > Ask yourselves, all of you, what power would hell have if those
>> imprisoned
>> > here could not dream of heaven?
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 9
>> > Date: Mon, 14 Mar 2016 15:28:52 +0000
>> > From: Sigurd Friis Truelsen <sigut.env.dtu.dk>
>> > Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> > whith paramfit
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
>> > Message-ID:
>> > <
>> > AFC3EDD6C86AD140AA9454795CA43DB20189CD84.ait-pex02mbx04.win.dtu.dk>
>> > Content-Type: text/plain; charset="iso-8859-1"
>> >
>> > Dear J?r?mie and Amber Users,
>> >
>> > >Dear Amber Users,
>> > >
>> > >I'm trying to improve angle parameters but paramfit seems not able to
>> > read angle parameters from the file which specify the parameters to fit.
>> > >This looks like an old issue that seems to have been fixed (
>> > http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
>> > 15.
>> > >When I specify only angle parameters, I get this message : ERROR IN
>> MAIN
>> > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> > >How to fix this bug?
>> > >
>> > >Thanks,
>> > >
>> > >J?r?mie Knoops
>> >
>> > I have the same problem when trying to fit angle parameters defined in a
>> > file. If only angles are to be fitted I get the ERROR message like yours.
>> > If I specify to fit everything in the file, Paramfit will perform the fit
>> > on bonds and dihedrals, but not on the angles.
>> > The only way I can get the angles to be fitted is to set
>> > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
>> > this is not necessarily desired.
>> > Did you find a solution for this problem?
>> >
>> > Best regards,
>> >
>> > Sigurd Truelsen
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 10
>> > Date: Mon, 14 Mar 2016 12:42:53 -0400
>> > From: David Cerutti <dscerutti.gmail.com>
>> > Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> > whith paramfit
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
>> > Message-ID:
>> > <CAEmzWj1jJceVTCnCSuWkDAGQ5xy1eqr=
>> > BBHeQrjRfvTTK5GrJQ.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Not sure what paramfit does with angle parameterization, but you should
>> > both give mdgx a shot. It's not enough to just reoptimize the
>> stiffnesses
>> > of the angle parameters, you need to get the equilibria in there as well.
>> > mdgx has the capability to do it all, plus any torsions you want, in a
>> > single run, so long as you have coordinates, energies, and an Amber
>> > topology for your system I can show you how to run the calculations.
>> > Really should get a parameter development tutorial for mdgx up on the
>> > website.
>> >
>> > Dave
>> >
>> >
>> > On Mon, Mar 14, 2016 at 11:28 AM, Sigurd Friis Truelsen <
>> sigut.env.dtu.dk>
>> > wrote:
>> >
>> > > Dear J?r?mie and Amber Users,
>> > >
>> > > >Dear Amber Users,
>> > > >
>> > > >I'm trying to improve angle parameters but paramfit seems not able to
>> > > read angle parameters from the file which specify the parameters to
>> fit.
>> > > >This looks like an old issue that seems to have been fixed (
>> > > http://archive.ambermd.org/201407/0481.html) , but I'm using
>> Ambertools
>> > > 15.
>> > > >When I specify only angle parameters, I get this message : ERROR IN
>> > MAIN
>> > > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> > > >How to fix this bug?
>> > > >
>> > > >Thanks,
>> > > >
>> > > >J?r?mie Knoops
>> > >
>> > > I have the same problem when trying to fit angle parameters defined in
>> a
>> > > file. If only angles are to be fitted I get the ERROR message like
>> yours.
>> > > If I specify to fit everything in the file, Paramfit will perform the
>> fit
>> > > on bonds and dihedrals, but not on the angles.
>> > > The only way I can get the angles to be fitted is to set
>> > > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted,
>> but
>> > > this is not necessarily desired.
>> > > Did you find a solution for this problem?
>> > >
>> > > Best regards,
>> > >
>> > > Sigurd Truelsen
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 11
>> > Date: Mon, 14 Mar 2016 13:19:39 -0500
>> > From: Balaji Selvam <bselvam01.gmail.com>
>> > Subject: [AMBER] parmed -setBond command
>> > To: amber.ambermd.org
>> > Message-ID:
>> > <
>> > CAMwUL-YMD3fdBRh+XXzGoksWd5wknCOCNZmdc0027zMA3hxgFA.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > Dear AMBER Users,
>> >
>> > I am trying to fix the OH bond length of the residue using parmed setBond
>> > command.
>> >
>> > I am using the following script
>> >
>> > parmed.py example.prmtop
>> >
>> > loadRestrt 99.rst
>> >
>> > setOverwrite True
>> >
>> > setBond :640.OG1 :640.HG1 100 0.96
>> >
>> > outparm test.prmtop test01.rst
>> >
>> >
>> > 640 is the residue number, 100 is the force constant and 0.96 is the
>> actual
>> > bond length.
>> >
>> >
>> > I am not changing the bond just trying the fix the actual bond length
>> using
>> > parmed.
>> >
>> >
>> > However, the script shows error as "AmberMask: Unrecognized symbol in
>> > residue name parsing".
>> >
>> >
>> > Kindly advice.
>> >
>> >
>> > Many Thanks
>> >
>> > Balaji
>> >
>> >
>> > ------------------------------
>> >
>> > Message: 12
>> > Date: Mon, 14 Mar 2016 12:36:04 -0600
>> > From: Daniel Roe <daniel.r.roe.gmail.com>
>> > Subject: Re: [AMBER] parmed -setBond command
>> > To: AMBER Mailing List <amber.ambermd.org>
>> > Message-ID:
>> > <CAAC0qOYtSrwuwWW7HwfY4Ctrdr9iUOM=
>> > HdN7e_rK4gzVZx3k6w.mail.gmail.com>
>> > Content-Type: text/plain; charset=UTF-8
>> >
>> > On Mon, Mar 14, 2016 at 12:19 PM, Balaji Selvam <bselvam01.gmail.com>
>> > wrote:
>> > > setBond :640.OG1 :640.HG1 100 0.96
>> >
>> > These are not valid Amber masks. The symbol for atom is '.', not '.'.
>> >
>> > ":640.OG1" etc will work. You may want to review Amber mask syntax;
>> > see sections 20.1 or 29.1.6 in the Amber15 manual.
>> >
>> > -Dan
>> >
>> > >
>> > > outparm test.prmtop test01.rst
>> > >
>> > >
>> > > 640 is the residue number, 100 is the force constant and 0.96 is the
>> > actual
>> > > bond length.
>> > >
>> > >
>> > > I am not changing the bond just trying the fix the actual bond length
>> > using
>> > > parmed.
>> > >
>> > >
>> > > However, the script shows error as "AmberMask: Unrecognized symbol in
>> > > residue name parsing".
>> > >
>> > >
>> > > Kindly advice.
>> > >
>> > >
>> > > Many Thanks
>> > >
>> > > Balaji
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> >
>> > --
>> > -------------------------
>> > Daniel R. Roe, PhD
>> > Department of Medicinal Chemistry
>> > University of Utah
>> > 30 South 2000 East, Room 307
>> > Salt Lake City, UT 84112-5820
>> > http://home.chpc.utah.edu/~cheatham/
>> > (801) 587-9652
>> > (801) 585-6208 (Fax)
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>> >
>> > End of AMBER Digest, Vol 1515, Issue 1
>> > **************************************
>> >
>>
>>
>> ------------------------------
>>
>> Message: 13
>> Date: Tue, 15 Mar 2016 06:58:52 -0700
>> From: David A Case <david.case.rutgers.edu>
>> Subject: Re: [AMBER] A query about using random seed generator in
>> simulations
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20160315135852.GB75828.scarletmail.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Tue, Mar 15, 2016, anu chandra wrote:
>> >
>> > I am using the following input parameters for doing the production run of
>> > classical MD simulation with Amber.
>> >
>> > imin = 0, ntx = 5, irest = 1,
>> > ntt =3, gamma_ln=2.0, ig=-1,
>> >
>> > Following a standard protocol, I did minimization and extensive (10-20
>> ns)
>> > equilibration of the protein-water system before entering to production
>> > run. But, I am a little confused about the use random seed generator in
>> > production. As per Amber manual, ig=-1 will generate different random
>> seed
>> > and thereby different staring velocity for each simulation window ( say
>> one
>> > use a 5 ns window for doing a 100 ns long simulation). Such a change in
>> > velocity can bring changes in the phase space for every run ( ie, the run
>> > may not be a continuation of previous window). If that the case, what is
>> > the point of doing extensive equilibration here?
>>
>> When you set irest=1, the initial velocities for that run are taken from
>> the
>> restart file, and no random number is used. For you case, the random
>> number
>> generator is only used for the Langevin integrator.
>>
>> ...hope this helps....dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 14
>> Date: Tue, 15 Mar 2016 08:31:19 -0600
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAAC0qOYDdRS684c8+tiNT0Wexy8O-Ep+3XdVzhbRvCn11fBXVg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> What version of cpptraj are you using?
>>
>> On Tue, Mar 15, 2016 at 6:54 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com>
>> wrote:
>> > Thank you very much Dan!
>> >
>> > As per your suggestion, I tried as follows:
>> >
>> > vector S1 center :1-27,65-139.CA,C,N,O
>> > vector S2 center :28-33,46-64.CA,C,N,O
>> > vector S3 center :140-175,265-332.CA,C,N,O
>> > vector S4 center :176-264.CA,C,N,O
>> > create vector_traj.nc S1 S2 S3 S4 vectraj trajfmt netcdf parmout
>> > vector_traj.parm7 noorigin
>> >
>> >
>> > I was expecting a pseuto-trajectory with four atoms (and one origin) but
>> I
>> > still get a single atom.
>> >
>> > Thanks,
>> > Hirdesh
>> >
>> > On Mon, Mar 14, 2016 at 8:00 PM, <amber-request.ambermd.org> wrote:
>> >
>> >> Send AMBER mailing list submissions to
>> >> amber.ambermd.org
>> >>
>> >> To subscribe or unsubscribe via the World Wide Web, visit
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >> or, via email, send a message with subject or body 'help' to
>> >> amber-request.ambermd.org
>> >>
>> >> You can reach the person managing the list at
>> >> amber-owner.ambermd.org
>> >>
>> >> When replying, please edit your Subject line so it is more specific
>> >> than "Re: Contents of AMBER digest..."
>> >>
>> >>
>> >> AMBER Mailing List Digest
>> >>
>> >> Today's Topics:
>> >>
>> >> 1. Re: pseudo trajectories for 4 centers of mass? (Daniel Roe)
>> >> 2. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> >> (inp=2 in &pb namelist) (Stefan Ivanov)
>> >> 3. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> >> (inp=2 in &pb namelist) (Ray Luo)
>> >> 4. Re: How is ?Gnonpolar computed in MMPBSA.py in AMBER 14?
>> >> (inp=2 in &pb namelist) (Stefan Ivanov)
>> >> 5. ISQBP 2016 meeting - registration opened! (Thomas Cheatham)
>> >> 6. Re: AMBER:neutralisation of non integral charges (Shilpa Gupta)
>> >> 7. Re: AMBER:neutralisation of non integral charges (Hannes Loeffler)
>> >> 8. bad atom type with MMPBSA decomposition? (Kenneth Huang)
>> >> 9. Re: Problems when trying to improve angle parameters whith
>> >> paramfit (Sigurd Friis Truelsen)
>> >> 10. Re: Problems when trying to improve angle parameters whith
>> >> paramfit (David Cerutti)
>> >> 11. parmed -setBond command (Balaji Selvam)
>> >> 12. Re: parmed -setBond command (Daniel Roe)
>> >>
>> >>
>> >> ----------------------------------------------------------------------
>> >>
>> >> Message: 1
>> >> Date: Sun, 13 Mar 2016 14:40:39 -0600
>> >> From: Daniel Roe <daniel.r.roe.gmail.com>
>> >> Subject: Re: [AMBER] pseudo trajectories for 4 centers of mass?
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <
>> >> CAAC0qOavS0Upk9-A9TbFKpo7t36+pqpX_VLga-0FeA3DL8pReg.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Hi,
>> >>
>> >> On Sun, Mar 13, 2016 at 11:57 AM, Hirdesh Kumar <hirdesh.iitd.gmail.com
>> >
>> >> wrote:
>> >> >
>> >> > It would be great if I can visualize four center of masses as a
>> "single"
>> >> > molecule in VMD.
>> >>
>> >> You can do this by writing your vector data as a pseudo trajectory via
>> >> 'vectraj', e.g.
>> >>
>> >> parm myparm.parm7
>> >> trajin mytraj.nc
>> >> vector V1 center <mask1>
>> >> vector V2 center <mask2>
>> >> vector V3 center <mask3>
>> >> vector V4 center <mask4>
>> >> create vector_traj.nc V1 V2 V3 V4 vectraj trajfmt netcdf \
>> >> parmout vector_traj.parm7 noorigin
>> >>
>> >> This will create a pseudo trajectory containing your vector data. To
>> >> ensure that this script works as-is you should use the GitHub beta
>> >> version of cpptraj. If you want to use the AmberTools version of
>> >> cpptraj do not include the 'noorigin' keyword since that is not yet
>> >> implemented in that version.
>> >>
>> >> Hope this helps,
>> >>
>> >> -Dan
>> >>
>> >> >
>> >> > Thanks,
>> >> > Hirdesh
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe, PhD
>> >> Department of Medicinal Chemistry
>> >> University of Utah
>> >> 30 South 2000 East, Room 307
>> >> Salt Lake City, UT 84112-5820
>> >> http://home.chpc.utah.edu/~cheatham/
>> >> (801) 587-9652
>> >> (801) 585-6208 (Fax)
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 2
>> >> Date: Mon, 14 Mar 2016 02:11:01 +0000
>> >> From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
>> >> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <58F9FB3DCABE5F4F905560AB46873D7C77320B04.MBXP05.ds.man.ac.uk>
>> >> Content-Type: text/plain; charset="iso-8859-7"
>> >>
>> >> Hi Prof Luo,
>> >>
>> >> Thank you very much for your helpful and informative reply.
>> >>
>> >> If I understand correctly, by default:
>> >>
>> >> ?Grepulsive = molecular_volume*? + c, where ? is the surface tension
>> and c
>> >> is the cavity offset, correct? How is the volume computed? More
>> precisely,
>> >> what volume is being used - solvent accessible (SAV) or solvent excluded
>> >> volume (SEV)?
>> >>
>> >> As for the keywords in the output:
>> >>
>> >>
>> >> EPB = ?Gelectrostatic
>> >> ENPOLAR = ?Gattractive (?Gdispersion)
>> >> ECAVITY = ?Grepulsive(?Gcavitation)
>> >>
>> >> and
>> >>
>> >> ?Gnonpolar = ENPOLAR + ECAVITY
>> >>
>> >> Finally,
>> >>
>> >> ?Gsolvation = ?Gnonpolar + EPB
>> >>
>> >> Is this correct?
>> >>
>> >> Best wishes,
>> >>
>> >> Stefan
>> >>
>> >>
>> >> ________________________________________
>> >> From: Ray Luo [rluo.uci.edu]
>> >> Sent: Sunday, March 13, 2016 4:21 AM
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >>
>> >> Hi Stefan,
>> >>
>> >> > I would like to ask a few questions regarding MMPBSA.py's
>> >> > implementation in AMBER14. Having read the AMBER14 manual, the
>> >> > MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> >> > bit confused and unsure about a few things.
>> >> >
>> >> > What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> >> > in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> >> > I'm specifically talking about the Poisson-Boltzmann computations,
>> i.e.
>> >> > inp=2 in the &pb namelist (which is equivalent to not specifying
>> >> > anything for inp, because 2 is the default value, right)?. I think the
>> >> > manual is a bit unclear. From what I understand
>> >>
>> >> This is correct.
>> >>
>> >> > ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> >> >
>> >> > and
>> >> >
>> >> > ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> >>
>> >> Yes, this is correct.
>> >>
>> >> > Finally:
>> >> >
>> >> > ?Grepulsive = ?*SASA + c
>> >>
>> >> The default behavior is that the repulsive free energy is modeled as
>> >> linearly depended on the volume within SASA since this is the best
>> >> observed scheme for the tested small molecules and side chain mutation
>> >> data.
>> >>
>> >> > where SASA is computed with the LCPO method. Is this correct or is
>> >> > the cavitation term proportional to molecular volume? If so, how is
>> that
>> >> > computed?
>> >>
>> >> If you choose to model it as linearly dependent on SASA, PBSA would
>> >> compute SASA numerically, it does not use the approximated LCPO
>> >> method.
>> >>
>> >> > Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> >> > EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> >> > the (repulsive) cavitation term and EDISPER is the (attractive)
>> >> > dispersion term (although in this case ENPOLAR is negative and
>> >> > ECAVITY is positive)?
>> >>
>> >> This is because the the printing of ECAVITY (inp=2) shares the same
>> >> routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> >> because they both use linearly functional models. The sander printout
>> >> is more informative.
>> >>
>> >> > Also, is the internal PBSA solver in sander linear or nonlinear?
>> >>
>> >> It's linear by default.
>> >>
>> >> > I have seen a lot of recommendations for the "perl" version of
>> >> > MMPBSA, but very little for MMPBSA.py. What settings would you
>> >> > recommend for doing Poisson-Boltzmann calculations on protein -
>> >> > protein complexes?
>> >>
>> >> The two scripts should give you the same results if you use the same
>> >> options. The difference is that the perl script uses sander, and the
>> >> python script uses nab by default. If you prefer, you can use the
>> >> sander option in the python script so you can choose all the &pb
>> >> keywords as described in the manual. Apparently it is too hard to
>> >> support all &pb keywords in either scripts.
>> >>
>> >> You may want to use inp=1 for protein-protein complexes because the
>> >> inp=2 was not optimized for macromolecular "ligand" binding, though we
>> >> are working on it.
>> >>
>> >> All the best,
>> >> Ray
>> >> --
>> >> Ray Luo, Ph.D.
>> >> Professor
>> >> Biochemistry, Molecular Biophysics, Chemical Physics,
>> >> Chemical and Biomedical Engineering
>> >> University of California, Irvine, CA 92697-3900
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 3
>> >> Date: Sun, 13 Mar 2016 20:52:30 -0700
>> >> From: Ray Luo <rluo.uci.edu>
>> >> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <
>> >> CAOg1T6Sev165TLOpeGutcdgD4ZWnufx7Q1eYgDsx0VZCbzEyPA.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Hi Stefan,
>> >>
>> >> > If I understand correctly, by default:
>> >> >
>> >> > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension
>> and
>> >> c is the cavity offset, correct? How is the volume computed? More
>> >> precisely, what volume is being used - solvent accessible (SAV) or
>> solvent
>> >> excluded volume (SEV)?
>> >>
>> >> Yes, and it uses SAV since it performs better as shown in the original
>> >> paper.
>> >>
>> >> > As for the keywords in the output:
>> >> >
>> >> > EPB = ?Gelectrostatic
>> >> > ENPOLAR = ?Gattractive (?Gdispersion)
>> >> > ECAVITY = ?Grepulsive(?Gcavitation)
>> >>
>> >> In the python script (please refer to your own output):
>> >>
>> >> ENPOLAR is the repulsive free energy; it's positive.
>> >> EDISPER is the attractive free energy; it's negative.
>> >>
>> >> > and
>> >> >
>> >> > ?Gnonpolar = ENPOLAR + ECAVITY
>> >>
>> >> Yes.
>> >>
>> >> > Finally,
>> >> >
>> >> > ?Gsolvation = ?Gnonpolar + EPB
>> >> >
>> >> > Is this correct?
>> >>
>> >> Yes.
>> >>
>> >> All the best,
>> >> Ray
>> >> --
>> >> Ray Luo, Ph.D.
>> >> Professor
>> >> Biochemistry, Molecular Biophysics, Chemical Physics,
>> >> Chemical and Biomedical Engineering
>> >> University of California, Irvine, CA 92697-3900
>> >>
>> >> > ________________________________________
>> >> > From: Ray Luo [rluo.uci.edu]
>> >> > Sent: Sunday, March 13, 2016 4:21 AM
>> >> > To: AMBER Mailing List
>> >> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in
>> AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >> >
>> >> > Hi Stefan,
>> >> >
>> >> >> I would like to ask a few questions regarding MMPBSA.py's
>> >> >> implementation in AMBER14. Having read the AMBER14 manual, the
>> >> >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> >> >> bit confused and unsure about a few things.
>> >> >>
>> >> >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> >> >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> >> >> I'm specifically talking about the Poisson-Boltzmann computations,
>> i.e.
>> >> >> inp=2 in the &pb namelist (which is equivalent to not specifying
>> >> >> anything for inp, because 2 is the default value, right)?. I think
>> the
>> >> >> manual is a bit unclear. From what I understand
>> >> >
>> >> > This is correct.
>> >> >
>> >> >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> >> >>
>> >> >> and
>> >> >>
>> >> >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> >> >
>> >> > Yes, this is correct.
>> >> >
>> >> >> Finally:
>> >> >>
>> >> >> ?Grepulsive = ?*SASA + c
>> >> >
>> >> > The default behavior is that the repulsive free energy is modeled as
>> >> > linearly depended on the volume within SASA since this is the best
>> >> > observed scheme for the tested small molecules and side chain mutation
>> >> > data.
>> >> >
>> >> >> where SASA is computed with the LCPO method. Is this correct or is
>> >> >> the cavitation term proportional to molecular volume? If so, how is
>> that
>> >> >> computed?
>> >> >
>> >> > If you choose to model it as linearly dependent on SASA, PBSA would
>> >> > compute SASA numerically, it does not use the approximated LCPO
>> >> > method.
>> >> >
>> >> >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> >> >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> >> >> the (repulsive) cavitation term and EDISPER is the (attractive)
>> >> >> dispersion term (although in this case ENPOLAR is negative and
>> >> >> ECAVITY is positive)?
>> >> >
>> >> > This is because the the printing of ECAVITY (inp=2) shares the same
>> >> > routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> >> > because they both use linearly functional models. The sander printout
>> >> > is more informative.
>> >> >
>> >> >> Also, is the internal PBSA solver in sander linear or nonlinear?
>> >> >
>> >> > It's linear by default.
>> >> >
>> >> >> I have seen a lot of recommendations for the "perl" version of
>> >> >> MMPBSA, but very little for MMPBSA.py. What settings would you
>> >> >> recommend for doing Poisson-Boltzmann calculations on protein -
>> >> >> protein complexes?
>> >> >
>> >> > The two scripts should give you the same results if you use the same
>> >> > options. The difference is that the perl script uses sander, and the
>> >> > python script uses nab by default. If you prefer, you can use the
>> >> > sander option in the python script so you can choose all the &pb
>> >> > keywords as described in the manual. Apparently it is too hard to
>> >> > support all &pb keywords in either scripts.
>> >> >
>> >> > You may want to use inp=1 for protein-protein complexes because the
>> >> > inp=2 was not optimized for macromolecular "ligand" binding, though we
>> >> > are working on it.
>> >> >
>> >> > All the best,
>> >> > Ray
>> >> > --
>> >> > Ray Luo, Ph.D.
>> >> > Professor
>> >> > Biochemistry, Molecular Biophysics, Chemical Physics,
>> >> > Chemical and Biomedical Engineering
>> >> > University of California, Irvine, CA 92697-3900
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 4
>> >> Date: Mon, 14 Mar 2016 05:11:33 +0000
>> >> From: Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk>
>> >> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <58F9FB3DCABE5F4F905560AB46873D7C77320B19.MBXP05.ds.man.ac.uk>
>> >> Content-Type: text/plain; charset="iso-8859-7"
>> >>
>> >> Hi Prof Luo,
>> >>
>> >> Many thanks and best wishes,
>> >>
>> >> Stefan
>> >>
>> >>
>> >> ________________________________________
>> >> From: Ray Luo [rluo.uci.edu]
>> >> Sent: Monday, March 14, 2016 3:52 AM
>> >> To: AMBER Mailing List
>> >> Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >>
>> >> Hi Stefan,
>> >>
>> >> > If I understand correctly, by default:
>> >> >
>> >> > ?Grepulsive = molecular_volume*? + c, where ? is the surface tension
>> and
>> >> c is the cavity offset, correct? How is the volume computed? More
>> >> precisely, what volume is being used - solvent accessible (SAV) or
>> solvent
>> >> excluded volume (SEV)?
>> >>
>> >> Yes, and it uses SAV since it performs better as shown in the original
>> >> paper.
>> >>
>> >> > As for the keywords in the output:
>> >> >
>> >> > EPB = ?Gelectrostatic
>> >> > ENPOLAR = ?Gattractive (?Gdispersion)
>> >> > ECAVITY = ?Grepulsive(?Gcavitation)
>> >>
>> >> In the python script (please refer to your own output):
>> >>
>> >> ENPOLAR is the repulsive free energy; it's positive.
>> >> EDISPER is the attractive free energy; it's negative.
>> >>
>> >> > and
>> >> >
>> >> > ?Gnonpolar = ENPOLAR + ECAVITY
>> >>
>> >> Yes.
>> >>
>> >> > Finally,
>> >> >
>> >> > ?Gsolvation = ?Gnonpolar + EPB
>> >> >
>> >> > Is this correct?
>> >>
>> >> Yes.
>> >>
>> >> All the best,
>> >> Ray
>> >> --
>> >> Ray Luo, Ph.D.
>> >> Professor
>> >> Biochemistry, Molecular Biophysics, Chemical Physics,
>> >> Chemical and Biomedical Engineering
>> >> University of California, Irvine, CA 92697-3900
>> >>
>> >> > ________________________________________
>> >> > From: Ray Luo [rluo.uci.edu]
>> >> > Sent: Sunday, March 13, 2016 4:21 AM
>> >> > To: AMBER Mailing List
>> >> > Subject: Re: [AMBER] How is ?Gnonpolar computed in MMPBSA.py in
>> AMBER
>> >> 14? (inp=2 in &pb namelist)
>> >> >
>> >> > Hi Stefan,
>> >> >
>> >> >> I would like to ask a few questions regarding MMPBSA.py's
>> >> >> implementation in AMBER14. Having read the AMBER14 manual, the
>> >> >> MMPBSA.py paper, and a few papers referenced in the manual, I'm a
>> >> >> bit confused and unsure about a few things.
>> >> >>
>> >> >> What is the default scheme for computing ?Gsolvation in MMPBSA.py
>> >> >> in AMBER 14 (default is inp = 2, according to the AMBER14 manual)?
>> >> >> I'm specifically talking about the Poisson-Boltzmann computations,
>> i.e.
>> >> >> inp=2 in the &pb namelist (which is equivalent to not specifying
>> >> >> anything for inp, because 2 is the default value, right)?. I think
>> the
>> >> >> manual is a bit unclear. From what I understand
>> >> >
>> >> > This is correct.
>> >> >
>> >> >> ?Gsolvation = ?Gelectrostatic + ?Gnonpolar
>> >> >>
>> >> >> and
>> >> >>
>> >> >> ?Gnonpolar = ?Grepulsive(?Gcavitation) + ?Gattractive (?Gdispersion).
>> >> >
>> >> > Yes, this is correct.
>> >> >
>> >> >> Finally:
>> >> >>
>> >> >> ?Grepulsive = ?*SASA + c
>> >> >
>> >> > The default behavior is that the repulsive free energy is modeled as
>> >> > linearly depended on the volume within SASA since this is the best
>> >> > observed scheme for the tested small molecules and side chain mutation
>> >> > data.
>> >> >
>> >> >> where SASA is computed with the LCPO method. Is this correct or is
>> >> >> the cavitation term proportional to molecular volume? If so, how is
>> that
>> >> >> computed?
>> >> >
>> >> > If you choose to model it as linearly dependent on SASA, PBSA would
>> >> > compute SASA numerically, it does not use the approximated LCPO
>> >> > method.
>> >> >
>> >> >> Here is a typical output file I get (see below). I see EPB, ENPOLAR,
>> >> >> EDISPER, but no ECAVITY term. Does this mean that ENPOLAR is
>> >> >> the (repulsive) cavitation term and EDISPER is the (attractive)
>> >> >> dispersion term (although in this case ENPOLAR is negative and
>> >> >> ECAVITY is positive)?
>> >> >
>> >> > This is because the the printing of ECAVITY (inp=2) shares the same
>> >> > routine as the printing ENPOLAR (inp=1) in the script. Again this is
>> >> > because they both use linearly functional models. The sander printout
>> >> > is more informative.
>> >> >
>> >> >> Also, is the internal PBSA solver in sander linear or nonlinear?
>> >> >
>> >> > It's linear by default.
>> >> >
>> >> >> I have seen a lot of recommendations for the "perl" version of
>> >> >> MMPBSA, but very little for MMPBSA.py. What settings would you
>> >> >> recommend for doing Poisson-Boltzmann calculations on protein -
>> >> >> protein complexes?
>> >> >
>> >> > The two scripts should give you the same results if you use the same
>> >> > options. The difference is that the perl script uses sander, and the
>> >> > python script uses nab by default. If you prefer, you can use the
>> >> > sander option in the python script so you can choose all the &pb
>> >> > keywords as described in the manual. Apparently it is too hard to
>> >> > support all &pb keywords in either scripts.
>> >> >
>> >> > You may want to use inp=1 for protein-protein complexes because the
>> >> > inp=2 was not optimized for macromolecular "ligand" binding, though we
>> >> > are working on it.
>> >> >
>> >> > All the best,
>> >> > Ray
>> >> > --
>> >> > Ray Luo, Ph.D.
>> >> > Professor
>> >> > Biochemistry, Molecular Biophysics, Chemical Physics,
>> >> > Chemical and Biomedical Engineering
>> >> > University of California, Irvine, CA 92697-3900
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 5
>> >> Date: Sun, 13 Mar 2016 23:15:46 -0600 (MDT)
>> >> From: Thomas Cheatham <tec3.utah.edu>
>> >> Subject: [AMBER] ISQBP 2016 meeting - registration opened!
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <alpine.OSX.2.20.1603132314110.7776.thomass-macbook-air-3.local
>> >
>> >> Content-Type: text/plain; charset="iso-8859-15"
>> >>
>> >>
>> >> ...opportunities for people to speak! --tec3
>> >>
>> >>
>> >> Dear colleagues,?
>> >>
>> >> We are thrilled to announce that the registration for the President's
>> >> Meeting 2016 of the International Society of Quantum Biology and
>> >> Pharmacology (ISQBP) is now opened!?
>> >>
>> >> The program will feature oral presentations by an exciting line up of
>> >> invited speakers (see list below). In addition we welcome abstract
>> >> submission for ca. 15 short oral presentations and ?posters, with a
>> focus
>> >> on the following topics: nucleic acids, enzyme catalysis, protein-lipid
>> >> interactions, methods development, protein dynamics and drug design.?
>> >>
>> >> Registration and abstract submission forms can be found
>> >> at?www.isqbp2016.org.
>> >>
>> >> DATE: 19-22 June 2016?
>> >>
>> >> PLACE: Grand Hotel Terminus, Bergen, Norway (www.grandterminus.no/en/).
>> >> The venue is conveniently located in the city center of Bergen, with
>> >> frequent transfer from the airport (30 minutes drive by airport bus or
>> >> taxi).
>> >>
>> >> INVITED SPEAKERS: Charles L. Brooks III, Thomas E. Cheatham III, Vlad
>> >> Cojoracu, Annick Dejaegere, Carmen Domene, William L. Jorgensen, Syma
>> >> Khalid, Carmay Lim, Alex MacKerell, Lennart Nilsson, Masha Niv, Modesto
>> >> Orozco, Montgomery Pettitt, Carol Post, Rebecca Wade
>> >>
>> >> ABSTRACTS: we are welcoming abstracts for ca. 15 short oral
>> presentations
>> >> and posters.
>> >>
>> >> IMPORTANT DATES:
>> >> Early bird registration until March 20th
>> >> Abstract submission deadline for talks: March 20th
>> >> Abstract submission deadline for posters: April 15th
>> >>
>> >> TRAVEL AWARDS: Two ISQBP travel awards will be provided by the Society
>> to
>> >> support students presenting their work at the meeting. The selection
>> will
>> >> be based on the creativity, relevance and quality of the work as well as
>> >> the distance the student has to travel to attend the conference.
>> >>
>> >> MEETING WEBSITE:?www.isqbp2016.org
>> >>
>> >> ISQBP: want to know more about the International Society of Quantum
>> >> Biology and Pharmacology? Visit our webpage at?
>> http://isqbp.umaryland.edu
>> >>
>> >>
>> >>
>> >>
>> >> With best regards,
>> >> The Scientific Committee
>> >>
>> >> Nathalie Reuter?
>> >> (Computational Biology Unit, University of Bergen)
>> >>
>> >> Bjorn Olav Brandsdal?
>> >> (Centre for Theoretical and Computational Chemistry, University of
>> Tromso)
>> >>
>> >> Michele Cascella
>> >> (Centre for Theoretical and Computational Chemistry, University of
>> Oslo)To
>> >> join or leave the
>> >> molecular-dynamics-news email list, go to:
>> >> http://www.jiscmail.ac.uk/lists/molecular-dynamics-news.html
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 6
>> >> Date: Mon, 14 Mar 2016 13:22:42 +0000 (UTC)
>> >> From: Shilpa Gupta <guptashilpa_91.yahoo.com>
>> >> Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
>> >> To: <amber.ambermd.org>
>> >> Message-ID:
>> >> <2032101966.923925.1457961762365.JavaMail.yahoo.mail.yahoo.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Dear Amber users,
>> >> i am getting non integral charges (19.994) on my macromolecule. How
>> >> can i neutralise the charge using addions in tleap. Thanks in advance.
>> >>
>> >>
>> >> Shilpa Gupta
>> >> University of Delhi
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 7
>> >> Date: Mon, 14 Mar 2016 13:37:42 +0000
>> >> From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
>> >> Subject: Re: [AMBER] AMBER:neutralisation of non integral charges
>> >> To: <amber.ambermd.org>
>> >> Cc: Shilpa Gupta <guptashilpa_91.yahoo.com>
>> >> Message-ID: <20160314133742.6d9c6ecb.zgb83773vig.dl.ac.uk>
>> >> Content-Type: text/plain; charset="US-ASCII"
>> >>
>> >> On Mon, 14 Mar 2016 13:22:42 +0000
>> >> Shilpa Gupta <guptashilpa_91.yahoo.com> wrote:
>> >>
>> >> > Dear Amber users,
>> >> > i am getting non integral charges (19.994) on my macromolecule.
>> >> > How can i neutralise the charge using addions in tleap. Thanks in
>> >> > advance.
>> >>
>> >> Type 'help addions' in leap and read the manual. I spotted an example
>> >> in the latter when I searched for 'neutralize'.
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 8
>> >> Date: Mon, 14 Mar 2016 09:58:25 -0400
>> >> From: Kenneth Huang <kennethneltharion.gmail.com>
>> >> Subject: [AMBER] bad atom type with MMPBSA decomposition?
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <
>> >> CALeh7kBZ2duQo0Eg2y2W0q_-rj-NBXufVcgSA3eAgk14NrcTjA.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Hi all,
>> >>
>> >> As the subject says, I'm running into a bad atom type error with
>> MMPBSA.
>> >> Specifically when I try to run decomposition- without decomposition, it
>> >> runs without any errors, but when I try to run decomp it exits after
>> >> initializing with the bad atom type error.
>> >>
>> >> I already had two modifications in mdread2.F90 which I thought would've
>> >> fixed the issue-
>> >>
>> >> ! Begin modifications
>> >> > else if (atype == 'K+') then
>> >> > x(l165-1+i) = 1.52d0 + 1.4d0
>> >> > x(l170-1+i) = 0.68563d0
>> >> > x(l175-1+i) = -0.1868d0
>> >> > x(l180-1+i) = -0.00135573d0
>> >> > x(l185-1+i) = 0.00023743d0
>> >> > ! End modifications
>> >> >
>> >>
>> >>
>> >> else if (atomicnumber .eq. 12) then
>> >> > ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys.
>> >> > 1997, 107, 5422
>> >> > ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys.
>> >> > 1997, 107, 5422
>> >> > ! Mg radius = 1.45A: Aqvist 1992
>> >> > x(L165-1+i) = 1.18d0 + 1.4d0
>> >> > ! Begin modifications
>> >> > else if (atomicnumber .eq. 19) then
>> >> > x(L165-1+i) = 1.52d0 + 1.4d0
>> >> > ! End modifications
>> >> > else
>> >> > write( 0,* ) 'bad atom type: ',atype,' cannot perform
>> >> >
>> >>
>> >> And I've double checked %FLAG ATOMIC_NUMBER in the topology files to
>> make
>> >> sure that the atomic number is correct (19), did a fresh install and
>> >> recompiled in serial and parallel with the changes to mdread2.f90, but
>> I'm
>> >> still getting the same error with my input as-
>> >>
>> >> &general
>> >> endframe=1000, interval=100, keep_files=2, verbose=1,
>> >> receptor_mask=':1-1044', ligand_mask=':1045-2088'
>> >> /
>> >> &gb
>> >> igb=2, saltcon=0.100,
>> >> /
>> >> &pb
>> >> istrng=0.100, indi=2.0, radiopt=0, inp=1,
>> >> /
>> >> &decomp
>> >> idecomp=1, print_res="12-24; 291-308; 330-342; 365-389"
>> >> dec_verbose=3,
>> >> /
>> >>
>> >> At this point, I'm kind of baffled as to why it'd throwing up the error
>> >> message since I can't find a discernible reason why it'd be tossing out
>> >> that message.
>> >>
>> >> Best,
>> >>
>> >> Kenneth
>> >> --
>> >> Ask yourselves, all of you, what power would hell have if those
>> imprisoned
>> >> here could not dream of heaven?
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 9
>> >> Date: Mon, 14 Mar 2016 15:28:52 +0000
>> >> From: Sigurd Friis Truelsen <sigut.env.dtu.dk>
>> >> Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> >> whith paramfit
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
>> >> Message-ID:
>> >> <
>> >> AFC3EDD6C86AD140AA9454795CA43DB20189CD84.ait-pex02mbx04.win.dtu.dk>
>> >> Content-Type: text/plain; charset="iso-8859-1"
>> >>
>> >> Dear J?r?mie and Amber Users,
>> >>
>> >> >Dear Amber Users,
>> >> >
>> >> >I'm trying to improve angle parameters but paramfit seems not able to
>> >> read angle parameters from the file which specify the parameters to fit.
>> >> >This looks like an old issue that seems to have been fixed (
>> >> http://archive.ambermd.org/201407/0481.html) , but I'm using Ambertools
>> >> 15.
>> >> >When I specify only angle parameters, I get this message : ERROR IN
>> MAIN
>> >> - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> >> >How to fix this bug?
>> >> >
>> >> >Thanks,
>> >> >
>> >> >J?r?mie Knoops
>> >>
>> >> I have the same problem when trying to fit angle parameters defined in a
>> >> file. If only angles are to be fitted I get the ERROR message like
>> yours.
>> >> If I specify to fit everything in the file, Paramfit will perform the
>> fit
>> >> on bonds and dihedrals, but not on the angles.
>> >> The only way I can get the angles to be fitted is to set
>> >> "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted, but
>> >> this is not necessarily desired.
>> >> Did you find a solution for this problem?
>> >>
>> >> Best regards,
>> >>
>> >> Sigurd Truelsen
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 10
>> >> Date: Mon, 14 Mar 2016 12:42:53 -0400
>> >> From: David Cerutti <dscerutti.gmail.com>
>> >> Subject: Re: [AMBER] Problems when trying to improve angle parameters
>> >> whith paramfit
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Cc: "jeremie.knoops.umons.ac.be" <jeremie.knoops.umons.ac.be>
>> >> Message-ID:
>> >> <CAEmzWj1jJceVTCnCSuWkDAGQ5xy1eqr=
>> >> BBHeQrjRfvTTK5GrJQ.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Not sure what paramfit does with angle parameterization, but you should
>> >> both give mdgx a shot. It's not enough to just reoptimize the
>> stiffnesses
>> >> of the angle parameters, you need to get the equilibria in there as
>> well.
>> >> mdgx has the capability to do it all, plus any torsions you want, in a
>> >> single run, so long as you have coordinates, energies, and an Amber
>> >> topology for your system I can show you how to run the calculations.
>> >> Really should get a parameter development tutorial for mdgx up on the
>> >> website.
>> >>
>> >> Dave
>> >>
>> >>
>> >> On Mon, Mar 14, 2016 at 11:28 AM, Sigurd Friis Truelsen <
>> sigut.env.dtu.dk>
>> >> wrote:
>> >>
>> >> > Dear J?r?mie and Amber Users,
>> >> >
>> >> > >Dear Amber Users,
>> >> > >
>> >> > >I'm trying to improve angle parameters but paramfit seems not able to
>> >> > read angle parameters from the file which specify the parameters to
>> fit.
>> >> > >This looks like an old issue that seems to have been fixed (
>> >> > http://archive.ambermd.org/201407/0481.html) , but I'm using
>> Ambertools
>> >> > 15.
>> >> > >When I specify only angle parameters, I get this message : ERROR IN
>> >> MAIN
>> >> > - NDIMENSIONS VALUE OF 0 IS LESS THAN 1
>> >> > >How to fix this bug?
>> >> > >
>> >> > >Thanks,
>> >> > >
>> >> > >J?r?mie Knoops
>> >> >
>> >> > I have the same problem when trying to fit angle parameters defined
>> in a
>> >> > file. If only angles are to be fitted I get the ERROR message like
>> yours.
>> >> > If I specify to fit everything in the file, Paramfit will perform the
>> fit
>> >> > on bonds and dihedrals, but not on the angles.
>> >> > The only way I can get the angles to be fitted is to set
>> >> > "PARAMETERS_TO_FIT" to "DEFAULT", and all parameters will be fitted,
>> but
>> >> > this is not necessarily desired.
>> >> > Did you find a solution for this problem?
>> >> >
>> >> > Best regards,
>> >> >
>> >> > Sigurd Truelsen
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >> >
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 11
>> >> Date: Mon, 14 Mar 2016 13:19:39 -0500
>> >> From: Balaji Selvam <bselvam01.gmail.com>
>> >> Subject: [AMBER] parmed -setBond command
>> >> To: amber.ambermd.org
>> >> Message-ID:
>> >> <
>> >> CAMwUL-YMD3fdBRh+XXzGoksWd5wknCOCNZmdc0027zMA3hxgFA.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> Dear AMBER Users,
>> >>
>> >> I am trying to fix the OH bond length of the residue using parmed
>> setBond
>> >> command.
>> >>
>> >> I am using the following script
>> >>
>> >> parmed.py example.prmtop
>> >>
>> >> loadRestrt 99.rst
>> >>
>> >> setOverwrite True
>> >>
>> >> setBond :640.OG1 :640.HG1 100 0.96
>> >>
>> >> outparm test.prmtop test01.rst
>> >>
>> >>
>> >> 640 is the residue number, 100 is the force constant and 0.96 is the
>> actual
>> >> bond length.
>> >>
>> >>
>> >> I am not changing the bond just trying the fix the actual bond length
>> using
>> >> parmed.
>> >>
>> >>
>> >> However, the script shows error as "AmberMask: Unrecognized symbol in
>> >> residue name parsing".
>> >>
>> >>
>> >> Kindly advice.
>> >>
>> >>
>> >> Many Thanks
>> >>
>> >> Balaji
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> Message: 12
>> >> Date: Mon, 14 Mar 2016 12:36:04 -0600
>> >> From: Daniel Roe <daniel.r.roe.gmail.com>
>> >> Subject: Re: [AMBER] parmed -setBond command
>> >> To: AMBER Mailing List <amber.ambermd.org>
>> >> Message-ID:
>> >> <CAAC0qOYtSrwuwWW7HwfY4Ctrdr9iUOM=
>> >> HdN7e_rK4gzVZx3k6w.mail.gmail.com>
>> >> Content-Type: text/plain; charset=UTF-8
>> >>
>> >> On Mon, Mar 14, 2016 at 12:19 PM, Balaji Selvam <bselvam01.gmail.com>
>> >> wrote:
>> >> > setBond :640.OG1 :640.HG1 100 0.96
>> >>
>> >> These are not valid Amber masks. The symbol for atom is '.', not '.'.
>> >>
>> >> ":640.OG1" etc will work. You may want to review Amber mask syntax;
>> >> see sections 20.1 or 29.1.6 in the Amber15 manual.
>> >>
>> >> -Dan
>> >>
>> >> >
>> >> > outparm test.prmtop test01.rst
>> >> >
>> >> >
>> >> > 640 is the residue number, 100 is the force constant and 0.96 is the
>> >> actual
>> >> > bond length.
>> >> >
>> >> >
>> >> > I am not changing the bond just trying the fix the actual bond length
>> >> using
>> >> > parmed.
>> >> >
>> >> >
>> >> > However, the script shows error as "AmberMask: Unrecognized symbol in
>> >> > residue name parsing".
>> >> >
>> >> >
>> >> > Kindly advice.
>> >> >
>> >> >
>> >> > Many Thanks
>> >> >
>> >> > Balaji
>> >> > _______________________________________________
>> >> > AMBER mailing list
>> >> > AMBER.ambermd.org
>> >> > http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >>
>> >> --
>> >> -------------------------
>> >> Daniel R. Roe, PhD
>> >> Department of Medicinal Chemistry
>> >> University of Utah
>> >> 30 South 2000 East, Room 307
>> >> Salt Lake City, UT 84112-5820
>> >> http://home.chpc.utah.edu/~cheatham/
>> >> (801) 587-9652
>> >> (801) 585-6208 (Fax)
>> >>
>> >>
>> >>
>> >> ------------------------------
>> >>
>> >> _______________________________________________
>> >> AMBER mailing list
>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>> >>
>> >> End of AMBER Digest, Vol 1515, Issue 1
>> >> **************************************
>> >>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 15
>> Date: Tue, 15 Mar 2016 08:42:37 -0600
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Attempting MC barostat change: Failed
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CAAC0qOY8-aV7nczios1dcN220FjbVX426rU6ki-0UOE89qKYNg.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi,
>>
>> My initial thought is that perhaps your system is not yet
>> well-equilibrated enough for production dynamics. Remember that the
>> tutorials should be treated as examples or guidelines of how to do
>> something. They do not necessarily represent a generally applicable
>> procedure (in fact, there is a warning in red in that lipid tutorial
>> you linked to that refers to this). You can't just plug in any system
>> to a tutorial and expect things to just work - you have to understand
>> what's going on "under the hood" as well.
>>
>> I recommend some analysis of your coordinates prior to the production
>> step. Look at the density, area per lipid, etc, and make sure that
>> these look like they are converging to reasonable values for your
>> system. If you think your system is equilibrated, try a shorter run
>> (nstlim=5000) and print out the energies more often (ntpr=1 to 10 or
>> so) to get a better idea for what may be going on.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Tue, Mar 15, 2016 at 6:51 AM, Michael Shokhen
>> <michael.shokhen.biu.ac.il> wrote:
>> > Dear Amber List experts,
>> >
>> >
>> > I have followed all protocols from TUTORIAL A16: An Amber Lipid Force
>> Field Tutorial: Lipid14<
>> http://ambermd.org/tutorials/advanced/tutorial16/index.html>
>> >
>> > for MD simulation and files preparing of my protein in membrane.
>> >
>> > I have successfully passed all steps but the last productive MD.
>> >
>> > I have used prod.in file that is a copy of the original 05_Prod.in<
>> http://ambermd.org/tutorials/advanced/tutorial16/include/05_Prod.in>
>> script in the command:
>> >
>> > nohup pmemd.cuda -O -i prod.in<http://prod.in> -o prod1.out -p
>> ../*.prmtop \
>> > -c ../4_/hold10.rst -r prod1.rst -x prod1.nc<http://prod1.nc> &
>> >
>> > Examining the MD output file I have observed an error message:
>> >
>> >
>> > Attempting MC barostat change: Failed
>> >
>> >
>> > Please find below a fragment of the output file with all details
>> >
>> > including the text of the used prod.in file.
>> >
>> >
>> > Please advise me what changes in the prod.in parameters
>> >
>> > should be used to resolve the problem.
>> >
>> >
>> > Thank you,
>> >
>> > Michael
>> >
>> >
>> >
>> > -------------------------------------------------------
>> > Amber 14 SANDER 2014
>> > -------------------------------------------------------
>> >
>> > | PMEMD implementation of SANDER, Release 14
>> >
>> > | Run on 03/15/2016 at 13:47:45
>> >
>> > | Executable path: pmemd.cuda
>> > | Working directory: /home/shokhen/Documents/5f5b/5_
>> > | Hostname: Unknown
>> > [-O]verwriting output
>> >
>> > File Assignments:
>> > | MDIN: prod.in
>> > | MDOUT: prod1.out
>> > | INPCRD: ../4_/hold10.rst
>> > | PARM: ../mc.prmtop
>> > | RESTRT: prod1.rst
>> > | REFC: refc
>> > | MDVEL: mdvel
>> > | MDEN: mden
>> > | MDCRD: prod1.nc
>> > | MDINFO: mdinfo
>> > | MDFRC: mdfrc
>> >
>> >
>> > Here is the input file:
>> >
>> > Protein Lipid production 310K 125ns
>> > &cntrl
>> > imin=0,
>> > ntx=5,
>> > irest=1,
>> > ntc=2,
>> > ntf=2,
>> > tol=0.0000001,
>> > nstlim=62500000,
>> > ntt=3,
>> > gamma_ln=1.0,
>> > temp0=303.0,
>> > ntpr=5000,
>> > ntwr=500000,
>> > ntwx=5000,
>> > dt=0.002,
>> > ig=-1,
>> > ntb=2,
>> > ntp=2,
>> > cut=10.0,
>> > ioutfm=1,
>> > ntxo=2,
>> > barostat=2,
>> > /
>> >
>> >
>> >
>> >
>> >
>> > Note: ig = -1. Setting random seed to 703795 based on wallclock time in
>> > microseconds.
>> >
>> > |--------------------- INFORMATION ----------------------
>> > | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
>> > | Version 14.0.1
>> > |
>> > | 06/20/2014
>> > |
>> > | Implementation by:
>> > | Ross C. Walker (SDSC)
>> > | Scott Le Grand (nVIDIA)
>> > |
>> > | CAUTION: The CUDA code is currently experimental.
>> > | You use it at your own risk. Be sure to
>> > | check ALL results carefully.
>> > |
>> > | Precision model in use:
>> > | [SPFP] - Mixed Single/Double/Fixed Point Precision.
>> > | (Default)
>> > |
>> > |--------------------------------------------------------
>> >
>> >
>> > |------------------- GPU DEVICE INFO --------------------
>> > |
>> > | CUDA_VISIBLE_DEVICES: not set
>> > | CUDA Capable Devices Detected: 2
>> > | CUDA Device ID in use: 0
>> > | CUDA Device Name: GeForce GTX TITAN
>> > | CUDA Device Global Mem Size: 6143 MB
>> > | CUDA Device Num Multiprocessors: 14
>> > | CUDA Device Core Freq: 0.88 GHz
>> > |
>> > |--------------------------------------------------------
>> >
>> >
>> > | Conditional Compilation Defines Used:
>> > | PUBFFT
>> > | BINTRAJ
>> > | CUDA
>> > | EMIL
>> >
>> > | Largest sphere to fit in unit cell has radius = 34.888
>> >
>> > | New format PARM file being parsed.
>> > | Version = 1.000 Date = 03/14/16 Time = 13:03:58
>> >
>> > | Note: 1-4 EEL scale factors are being read from the topology file.
>> >
>> > | Note: 1-4 VDW scale factors are being read from the topology file.
>> > | Duplicated 0 dihedrals
>> >
>> > | Duplicated 0 dihedrals
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 1. RESOURCE USE:
>> >
>> --------------------------------------------------------------------------------
>> >
>> > getting box info from netcdf restart file
>> > NATOM = 48860 NTYPES = 24 NBONH = 39447 MBONA = 9250
>> > NTHETH = 33060 MTHETA = 10615 NPHIH = 53704 MPHIA = 35939
>> > NHPARM = 0 NPARM = 0 NNB = 162244 NRES = 9308
>> > NBONA = 9250 NTHETA = 10615 NPHIA = 35939 NUMBND = 88
>> > NUMANG = 194 NPTRA = 253 NATYP = 53 NPHB = 1
>> > IFBOX = 1 NMXRS = 50 IFCAP = 0 NEXTRA = 0
>> > NCOPY = 0
>> >
>> > | Coordinate Index Table dimensions: 14 12 15
>> > | Direct force subcell size = 5.5488 5.8147 5.8347
>> >
>> > BOX TYPE: RECTILINEAR
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 2. CONTROL DATA FOR THE RUN
>> >
>> --------------------------------------------------------------------------------
>> >
>> > default_name
>> >
>> > General flags:
>> > imin = 0, nmropt = 0
>> >
>> > Nature and format of input:
>> > ntx = 5, irest = 1, ntrx = 1
>> >
>> > Nature and format of output:
>> > ntxo = 2, ntpr = 5000, ntrx = 1, ntwr =
>> 500000
>> > iwrap = 0, ntwx = 5000, ntwv = 0, ntwe =
>> 0
>> > ioutfm = 1, ntwprt = 0, idecomp = 0,
>> rbornstat= 0
>> >
>> > Potential function:
>> > ntf = 2, ntb = 2, igb = 0, nsnb =
>> 25
>> > ipol = 0, gbsa = 0, iesp = 0
>> > dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>> >
>> > Frozen or restrained atoms:
>> > ibelly = 0, ntr = 0
>> >
>> > Molecular dynamics:
>> > nstlim = 62500000, nscm = 1000, nrespa = 1
>> > t = 0.00000, dt = 0.00200, vlimit = -1.00000
>> >
>> > Langevin dynamics temperature regulation:
>> > ig = 703795
>> > temp0 = 303.00000, tempi = 0.00000, gamma_ln= 1.00000
>> >
>> > Pressure regulation:
>> > ntp = 2
>> > pres0 = 1.00000, comp = 44.60000, taup = 1.00000
>> > Monte-Carlo Barostat:
>> > mcbarint = 100
>> >
>> > SHAKE:
>> > ntc = 2, jfastw = 0
>> > tol = 0.00000
>> >
>> > | Intermolecular bonds treatment:
>> > | no_intermolecular_bonds = 1
>> >
>> > | Energy averages sample interval:
>> > | ene_avg_sampling = 5000
>> >
>> > Ewald parameters:
>> > verbose = 0, ew_type = 0, nbflag = 1, use_pme =
>> 1
>> > vdwmeth = 1, eedmeth = 1, netfrc = 1
>> > Box X = 77.683 Box Y = 69.776 Box Z = 87.521
>> > Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>> > NFFT1 = 80 NFFT2 = 72 NFFT3 = 96
>> > Cutoff= 10.000 Tol =0.100E-04
>> > Ewald Coefficient = 0.27511
>> > Interpolation order = 4
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 3. ATOMIC COORDINATES AND VELOCITIES
>> >
>> --------------------------------------------------------------------------------
>> >
>> > default_name
>> > begin time read from input coords = 5420.000 ps
>> >
>> >
>> > Number of triangulated 3-point waters found: 8585
>> >
>> > Sum of charges from parm topology file = -0.00048135
>> > Forcing neutrality...
>> >
>> > | Dynamic Memory, Types Used:
>> > | Reals 1953878
>> > | Integers 3235415
>> >
>> > | Nonbonded Pairs Initial Allocation: 14778928
>> >
>> > | GPU memory information (estimate):
>> > | KB of GPU memory in use: 327439
>> > | KB of CPU memory in use: 69715
>> >
>> >
>> --------------------------------------------------------------------------------
>> > 4. RESULTS
>> >
>> --------------------------------------------------------------------------------
>> >
>> > ---------------------------------------------------
>> > APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>> > using 5000.0 points per unit in tabled values
>> > TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> > | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>> > | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>> > ---------------------------------------------------
>> > |---------------------------------------------------
>> > | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>> > | with 50.0 points per unit in tabled values
>> > | Relative Error Limit not exceeded for r .gt. 2.33
>> > | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>> > | with 50.0 points per unit in tabled values
>> > | Relative Error Limit not exceeded for r .gt. 2.80
>> > |---------------------------------------------------
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | MC Barostat: Decreasing size of volume moves
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | MC Barostat: Decreasing size of volume moves
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Succeeded
>> > | Attempting MC barostat change: Failed
>> > | MC Barostat: Decreasing size of volume moves
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Succeeded
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | MC Barostat: Decreasing size of volume moves
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Failed
>> > | Attempting MC barostat change: Succeeded
>> > | Attempting MC barostat change: Failed
>> > | MC Barostat: Decreasing size of volume moves
>> >
>> > NSTEP = 5000 TIME(PS) = 5430.000 TEMP(K) = 302.62 PRESS =
>> 0.0
>> > Etot = -76479.2165 EKtot = 32212.5273 EPtot =
>> -108691.7438
>> > BOND = 3129.9050 ANGLE = 12010.4285 DIHED =
>> 8922.3943
>> > 1-4 NB = 3003.3686 1-4 EEL = 19841.7423 VDWAALS =
>> 2219.1152
>> > EELEC = -157818.6978 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> > EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
>> 473431.6153
>> > Density =
>> 1.0263
>> >
>> ------------------------------------------------------------------------------
>> >
>> >
>> > <
>> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
>> >
>> >
>> >
>> > <
>> https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il
>> >
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
>>
>> ------------------------------
>>
>> Message: 16
>> Date: Tue, 15 Mar 2016 09:49:32 -0700
>> From: Niel Henriksen <shireham.gmail.com>
>> Subject: Re: [AMBER] Attempting MC barostat change: Failed
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <
>> CADtp_FuWeW2jjupPW5B8Qog1dFkBpSgqhpXCGvF3T7Mu1Tpw4A.mail.gmail.com>
>> Content-Type: text/plain; charset=UTF-8
>>
>> Hi Michael,
>>
>> In addition to Dan's recommendations, I'll just point out that the
>> "Attempting MC barostat change: Failed" message itself is not an error.
>> Such messages just indicate whether the MC barostat changed the box size
>> ("Success") or not ("Failed"), and a well-behaved simulation will have both
>> messages.
>>
>> Did you post the entire mdout file? If it really crashed at 5000 steps,
>> then proceed with Dan's suggestions. But if the simulation completed
>> normally, you do not need to worry about the MC barostat messages.
>>
>> --Niel
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> End of AMBER Digest, Vol 1516, Issue 1
>> **************************************
>>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 16 2016 - 10:30:03 PDT
