**
Cpptraj version:
CPPTRAJ: Trajectory Analysis. V15.00
On Tue, Mar 15, 2016 at 8:00 PM, <amber-request.ambermd.org> wrote:
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> 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 --------------
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>
> ------------------------------
>
> 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
> **************************************
>
_______________________________________________
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http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 16 2016 - 10:00:05 PDT
