Dear Dr. Case,
There is no solvent in my system. It is a system of Ionomers with the lithium ions (Ionomer melt). I used several smaller library files to put together a PDB file (AddToBox program) and to make it a periodic system, I used setBox program to generate parmtop and crd file in the Xleap (parm99 for Li parameters and GAFF). I am unable to send those files to current email address due to the file size restrictions, is there an alternate email ID I can send it to ?
Thanks,
Arjun
On Feb 9, 2014, at 2:00 PM, amber-request.ambermd.org wrote:
> Send AMBER mailing list submissions to
> amber.ambermd.org
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lists.ambermd.org/mailman/listinfo/amber
> or, via email, send a message with subject or body 'help' to
> amber-request.ambermd.org
>
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>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of AMBER digest..."
>
>
> AMBER Mailing List Digest
>
> Today's Topics:
>
> 1. Re: XLeap in Cygwin - Does it work? (Daniel Roe)
> 2. Re: XLeap in Cygwin - Does it work? (Ilyas Yildirim)
> 3. Re: AMBER Digest, Vol 759, Issue 1 (Arjun Sharma)
> 4. Re: AMBER Digest, Vol 759, Issue 1 (David A Case)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 8 Feb 2014 14:30:19 -0700
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Subject: Re: [AMBER] XLeap in Cygwin - Does it work?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID:
> <CAAC0qObwe8d-8PeXL6ZtmRVzGF-Gaf5ZdfaTV_cgMb0T2tDtVQ.mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
>
> I'm able to use xleap under cygwin with no issues. One question - did you
> recompile xleap after updating cygwin? It's possible that if certain X11
> libraries were updated that xleap may need to be re-compiled as well.
>
> -Dan
>
>
> On Sat, Feb 8, 2014 at 7:16 AM, Ilyas Yildirim
> <i-yildirim.northwestern.edu>wrote:
>
>> I have installed AMBER ver. 11 to my laptop a year ago (I think) so that I
>> can prepare systems using Leap Module. Since I've updated the cygwin to
>> x86 version, I am seeing that xleap is having some issues.
>>
>> First of all, when xleap is started and the XLEaP window is on focus
>> nothing can be written inside that window; the commands entered shows up
>> in the terminal. Focusing back the terminal and then coming back to Xleap
>> window corrects this problem. But now, I cannot use the shortcuts such as
>> the usage of ctrl key (to rotate, zoom, etc.).
>>
>> I am wondering if it is me or if this is a general issue when
>> setup-x86.exe of cygwin is used to install CYGWIN packages. Thanks.
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Department of Chemistry - 2145 Sheridan Road =
>> = Northwestern University - Evanston, IL 60208 =
>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>> = Website : http://ilyasyildirim.wordpress.com =
>> = ------------------------------------------------------- =
>> = http://www.linkedin.com/in/yildirimilyas =
>> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
>> -----------------------------------------------------------
>>
>>
>> _______________________________________________
>> 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 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 8 Feb 2014 15:34:48 -0600 (CST)
> From: Ilyas Yildirim <i-yildirim.northwestern.edu>
> Subject: Re: [AMBER] XLeap in Cygwin - Does it work?
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <alpine.LRH.2.03.1402081533320.29269.northwestern.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Indeed I recompiled AmberTools all, but still xleap behaves erratic.
>
> Ilyas Yildirim, Ph.D.
> -----------------------------------------------------------
> = Department of Chemistry - 2145 Sheridan Road =
> = Northwestern University - Evanston, IL 60208 =
> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
> = Website : http://ilyasyildirim.wordpress.com =
> = ------------------------------------------------------- =
> = http://www.linkedin.com/in/yildirimilyas =
> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
> -----------------------------------------------------------
>
>
> On Sat, 8 Feb 2014, Daniel Roe wrote:
>
>> Hi,
>>
>> I'm able to use xleap under cygwin with no issues. One question - did you
>> recompile xleap after updating cygwin? It's possible that if certain X11
>> libraries were updated that xleap may need to be re-compiled as well.
>>
>> -Dan
>>
>>
>> On Sat, Feb 8, 2014 at 7:16 AM, Ilyas Yildirim
>> <i-yildirim.northwestern.edu>wrote:
>>
>>> I have installed AMBER ver. 11 to my laptop a year ago (I think) so that I
>>> can prepare systems using Leap Module. Since I've updated the cygwin to
>>> x86 version, I am seeing that xleap is having some issues.
>>>
>>> First of all, when xleap is started and the XLEaP window is on focus
>>> nothing can be written inside that window; the commands entered shows up
>>> in the terminal. Focusing back the terminal and then coming back to Xleap
>>> window corrects this problem. But now, I cannot use the shortcuts such as
>>> the usage of ctrl key (to rotate, zoom, etc.).
>>>
>>> I am wondering if it is me or if this is a general issue when
>>> setup-x86.exe of cygwin is used to install CYGWIN packages. Thanks.
>>>
>>> Ilyas Yildirim, Ph.D.
>>> -----------------------------------------------------------
>>> = Department of Chemistry - 2145 Sheridan Road =
>>> = Northwestern University - Evanston, IL 60208 =
>>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>>> = Website : http://ilyasyildirim.wordpress.com =
>>> = ------------------------------------------------------- =
>>> = http://www.linkedin.com/in/yildirimilyas =
>>> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
>>> -----------------------------------------------------------
>>>
>>>
>>> _______________________________________________
>>> 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 201
>> 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
>>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Sat, 8 Feb 2014 17:15:02 -0600
> From: Arjun Sharma <arjunsharma83.gmail.com>
> Subject: Re: [AMBER] AMBER Digest, Vol 759, Issue 1
> To: amber.ambermd.org
> Message-ID: <ECB7E711-CD27-4598-A9EB-6FFF1C08729C.gmail.com>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear Dr. Case,
>
> Thanks for the reply. It usually crashes at the 81st step of 100 step minimization. However, it does work when maxcyc = nyc in minimization script. I am not sure if that is the right way to minimize.
>
> This is a periodic simulation. I am attaching the mdout file. Do let me know if you need more information.
>
> Thanks,
>
> Arjun
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>
>
>
> On Feb 8, 2014, at 2:00 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. sander minimization issue (Arjun Sharma)
>> 2. Re: sander minimization issue (David A Case)
>> 3. Re: Modifying Gaussian input files for the RED Server (FyD)
>> 4. Could not find target 281.850000 in any of the replica
>> trajectories (sunita.tifrh.res.in)
>> 5. XLeap in Cygwin - Does it work? (Ilyas Yildirim)
>> 6. Re: Could not find target 281.850000 in any of the replica
>> trajectories (Daniel Roe)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 7 Feb 2014 15:38:45 -0600
>> From: Arjun Sharma <arjunsharma83.gmail.com>
>> Subject: [AMBER] sander minimization issue
>> To: amber.ambermd.org
>> Message-ID: <DFD8678A-31A2-48A6-A7FF-597160AB8ECC.gmail.com>
>> Content-Type: text/plain; charset=windows-1252
>>
>> Dear Amber users,
>>
>> I have trouble running short minimization steps in sander for the coordinate file I generated using the Xleap. This is the error message :
>>
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>> Image PC Routine Line Source
>> sander 00000000004F94FA Unknown Unknown Unknown
>> sander 00000000006C3385 Unknown Unknown Unknown
>> sander 00000000004AAC12 Unknown Unknown Unknown
>> sander 0000000000498EFC Unknown Unknown Unknown
>> sander 000000000049431B Unknown Unknown Unknown
>> sander 000000000040C42C Unknown Unknown Unknown
>> libc.so.6 000000346EF1C4CB Unknown Unknown Unknown
>> sander 000000000040C35A Unknown Unknown Unknown
>>
>> I use the following minimization script
>> &cntrl
>> imin=1, maxcyc=100
>> ntpr=1,
>> ntr=0,
>> ntmin=1,
>> ncyc=50,
>> &end
>> END
>>
>> I did check the archives and tried certain things as suggested but it didn?t help my problem.I would appreciate your input.
>>
>> Thanks,
>> Arjun
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Fri, 7 Feb 2014 21:06:21 -0500
>> From: David A Case <case.biomaps.rutgers.edu>
>> Subject: Re: [AMBER] sander minimization issue
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20140208020503.GA8145.biomaps.rutgers.edu>
>> Content-Type: text/plain; charset=us-ascii
>>
>> On Fri, Feb 07, 2014, Arjun Sharma wrote:
>>>
>>> I have trouble running short minimization steps in sander
>>
>> Can you post the mdout file from this run? Among other things, that will
>> tell us what version of sander you are using, and how far the calculation got.
>> Is there any evidence of problems in that file?
>>
>> Is this a periodic simulation? If not, you need to set ntb=0 in the input
>> file?
>>
>> I could make more guesses, but that is probably not very helpful until
>> we have more information.
>>
>> ...dac
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 3
>> Date: Sat, 08 Feb 2014 07:42:11 +0100
>> From: FyD <fyd.q4md-forcefieldtools.org>
>> Subject: Re: [AMBER] Modifying Gaussian input files for the RED Server
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID: <20140208074211.5fzjwlfioc4sc0ow.webmail.u-picardie.fr>
>> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
>> format="flowed"
>>
>> Dear Kamali,
>>
>> I look at the P10536 and from I saw all worked well and the QM output
>> you provided as inputs was recognized... No the Frequency job is not
>> used by R.E.D. IV. (It is used by R.E.D. Python when using the Complex
>> mode; improved in the next version).
>>
>> Pay attention to your input conformation; you could look in REDDB to
>> get examples of minima obtained for nucleosides (2 deoxy or not 2
>> deoxy).
>>
>> go at: http://q4md-forcefieldtools.org/REDDB/download.php
>>
>> Search project(s) by
>> -- R.E.DD.B. code (if known)
>> -- Molecule keyword *
>> -- Molecule name
>> -- Author lastname
>> -- Theory level/Basis set
>> Text RNA
>>
>> Search... [Done]
>> Result(s) for search by Molecule keyword RNA
>> Project name Nucleoside
>> Project code W-74
>> [...]
>> Project name Nucleoside
>> Project code W-78
>> Project name Ribonucleic acid
>> Project code F-51
>> etc...
>>
>> You did not generate any fragment in this job.
>>
>> If you use RED Python if you do provide PDB + QM output files (the
>> next version of RED Python will recognize Gaussian job with Freq) set
>> MOLECULE1-ATMREORDR = OFF
>> in the Project.config to avoid atom reordering.
>>
>> regards, Francois
>>
>>
>>> I am trying to use the RED server to generate charges for a nucleoside with
>>> 5'OH and 3'OH termini, and I am emailing you about my job P10536. I
>>> submitted my own Gaussian output with this job. Because I have had errors
>>> in my RED Server jobs before for not properly removing frequency jobs from
>>> the output, I simply left out the Freq keyword in my Gaussian input script
>>> when calculating geometry optimization:
>>>
>>> *%Chk=Your-chkfile.chk*
>>> *%Mem=256MB*
>>> *%NProc=1*
>>>
>>> *#P hf/6-31G* Opt=(Tight,CalcFC) SCF(Conver=8) Test*
>>>
>>> *Gaussian optimization output to be used by R.E.D.*
>>> *...*
>>>
>>> The resulting output from this job is what I submitted with my p2n file in
>>> job P10536.
>>>
>>> I'm emailing to ask if it is all right to just leave out the Freq keyword
>>> like this, or does the RED Server rely on some part of the force constant
>>> calculations?
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 4
>> Date: Sat, 8 Feb 2014 17:09:30 +0530
>> From: sunita.tifrh.res.in
>> Subject: [AMBER] Could not find target 281.850000 in any of the
>> replica trajectories
>> To: amber.ambermd.org
>> Message-ID:
>> <ee728da59ddb2db7c82d6d126a1df68f.squirrel.webmail.tifrh.res.in>
>> Content-Type: text/plain;charset=iso-8859-1
>>
>> Hi amber users,
>>
>> I performed REMD simulations using AMBER10. I would like to filter
>> temperature trajectory. I have now AMBER12 so trying to extract with this
>> version. Earlier I filtered few temperatures from the same trajectories.
>> It worked at that time. Now I want to filter all the sixteen temperatures
>> and getting the problem. It is the version problem?
>>
>> Could anybody suggest why am I getting such message in spite of having
>> that temperature. I tried with all the sixteen temperatures. However
>> getting the same message.
>>
>> I pasted the messages I got when I ran the ptraj program.
>>
>> I will appreciate your help.
>>
>> Thank you.
>> Sunita
>> ======================================================
>>
>> PTRAJ: Processing input from "STDIN" ...
>>
>> PTRAJ: trajin remd_0.4ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>> Checking coordinates: remd_0.4ns.mdcrd.001
>> REMDTRAJ: Using specified file as lowest replica: remd_0.4ns.mdcrd.001
>> REMDTRAJ: Frames at 281.850000 K will be processed.
>> REMDTRAJ: Scanning for other REMD files.
>> REMDTRAJ: Found 1 replica traj files.
>>
>> PTRAJ: trajin remd_0.8ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>> Checking coordinates: remd_0.8ns.mdcrd.001
>> REMDTRAJ: Using specified file as lowest replica: remd_0.8ns.mdcrd.001
>> REMDTRAJ: Frames at 281.850000 K will be processed.
>> REMDTRAJ: Scanning for other REMD files.
>> REMDTRAJ: Found 1 replica traj files.
>>
>> PTRAJ: trajin remd_1.2ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>> Checking coordinates: remd_1.2ns.mdcrd.001
>> REMDTRAJ: Using specified file as lowest replica: remd_1.2ns.mdcrd.001
>> REMDTRAJ: Frames at 281.850000 K will be processed.
>> REMDTRAJ: Scanning for other REMD files.
>> REMDTRAJ: Found 1 replica traj files.
>>
>> PTRAJ: trajin remd_1.6ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>> Checking coordinates: remd_1.6ns.mdcrd.001
>> REMDTRAJ: Using specified file as lowest replica: remd_1.6ns.mdcrd.001
>> REMDTRAJ: Frames at 281.850000 K will be processed.
>> REMDTRAJ: Scanning for other REMD files.
>> REMDTRAJ: Found 1 replica traj files.
>>
>> PTRAJ: trajin remd_2.0ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>> Checking coordinates: remd_2.0ns.mdcrd.001
>> REMDTRAJ: Using specified file as lowest replica: remd_2.0ns.mdcrd.001
>> REMDTRAJ: Frames at 281.850000 K will be processed.
>> REMDTRAJ: Scanning for other REMD files.
>> REMDTRAJ: Found 1 replica traj files.
>>
>> PTRAJ: trajout output_remd_281.85.mdcrd
>> remd_0.4ns.mdcrd.001: 200 frames.
>> remd_0.8ns.mdcrd.001: 200 frames.
>> remd_1.2ns.mdcrd.001: 200 frames.
>> remd_1.6ns.mdcrd.001: 200 frames.
>> remd_2.0ns.mdcrd.001: 200 frames.
>>
>> PTRAJ: Successfully read the input file.
>> Coordinate processing will occur on 1000 frames.
>> Summary of I/O and actions follows:
>>
>> INPUT COORDINATE FILES
>> File (remd_0.4ns.mdcrd.001) is an AMBER REMD (new format) trajectory
>> with 200 sets
>> Replica processing by temperature will occur.
>> 1 files total (First index is 001), frames at 281.850000 K will be used.
>> File (remd_0.8ns.mdcrd.001) is an AMBER REMD (new format) trajectory
>> with 200 sets
>> Replica processing by temperature will occur.
>> 1 files total (First index is 001), frames at 281.850000 K will be used.
>> File (remd_1.2ns.mdcrd.001) is an AMBER REMD (new format) trajectory
>> with 200 sets
>> Replica processing by temperature will occur.
>> 1 files total (First index is 001), frames at 281.850000 K will be used.
>> File (remd_1.6ns.mdcrd.001) is an AMBER REMD (new format) trajectory
>> with 200 sets
>> Replica processing by temperature will occur.
>> 1 files total (First index is 001), frames at 281.850000 K will be used.
>> File (remd_2.0ns.mdcrd.001) is an AMBER REMD (new format) trajectory
>> with 200 sets
>> Replica processing by temperature will occur.
>> 1 files total (First index is 001), frames at 281.850000 K will be used.
>>
>> OUTPUT COORDINATE FILE
>> File (output_remd_281.85.mdcrd) is an AMBER trajectory
>> NO ACTIONS WERE SPECIFIED
>>
>> Processing AMBER REMD trajectory (new format)
>>
>> REMDTRAJ: Opening files remd_0.4ns.mdcrd.001 -> remd_0.4ns.mdcrd.001
>> Done.
>> 1%
>> REMDTRAJ: Final repTemp value read= 285.390000, set 3
>> Could not find target 281.850000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found in
>> traj! 100%
>>
>> Processing AMBER REMD trajectory (new format)
>>
>> REMDTRAJ: Opening files remd_0.8ns.mdcrd.001 -> remd_0.8ns.mdcrd.001
>> Done.
>>
>> REMDTRAJ: Final repTemp value read= 303.770000, set 1
>> Could not find target 281.850000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found in
>> traj! 100%
>>
>> Processing AMBER REMD trajectory (new format)
>>
>> REMDTRAJ: Opening files remd_1.2ns.mdcrd.001 -> remd_1.2ns.mdcrd.001
>> Done.
>>
>> REMDTRAJ: Final repTemp value read= 339.880000, set 1
>> Could not find target 281.850000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found in
>> traj! 100%
>>
>> Processing AMBER REMD trajectory (new format)
>>
>> REMDTRAJ: Opening files remd_1.6ns.mdcrd.001 -> remd_1.6ns.mdcrd.001
>> Done.
>>
>> REMDTRAJ: Final repTemp value read= 339.880000, set 1
>> Could not find target 281.850000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found in
>> traj! 100%
>>
>> Processing AMBER REMD trajectory (new format)
>>
>> REMDTRAJ: Opening files remd_2.0ns.mdcrd.001 -> remd_2.0ns.mdcrd.001
>> Done.
>>
>> REMDTRAJ: Final repTemp value read= 339.880000, set 1
>> Could not find target 281.850000 in any of the replica trajectories.
>> Check that all replica trajectory files were found and that
>> none of the trajectories are corrupted (e.g. missing a temperature).
>> ptrajProcessInputCoordinates(): Target replica temperature not found in
>> traj! 100%
>>
>>
>> PTRAJ: Successfully read in 2 sets and processed 2 sets.
>>
>> Dumping accumulated results (if any)
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 5
>> Date: Sat, 8 Feb 2014 08:16:30 -0600 (CST)
>> From: Ilyas Yildirim <i-yildirim.northwestern.edu>
>> Subject: [AMBER] XLeap in Cygwin - Does it work?
>> To: amber.ambermd.org
>> Message-ID: <alpine.LRH.2.03.1402080810480.26674.northwestern.edu>
>> Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII
>>
>> I have installed AMBER ver. 11 to my laptop a year ago (I think) so that I
>> can prepare systems using Leap Module. Since I've updated the cygwin to
>> x86 version, I am seeing that xleap is having some issues.
>>
>> First of all, when xleap is started and the XLEaP window is on focus
>> nothing can be written inside that window; the commands entered shows up
>> in the terminal. Focusing back the terminal and then coming back to Xleap
>> window corrects this problem. But now, I cannot use the shortcuts such as
>> the usage of ctrl key (to rotate, zoom, etc.).
>>
>> I am wondering if it is me or if this is a general issue when
>> setup-x86.exe of cygwin is used to install CYGWIN packages. Thanks.
>>
>> Ilyas Yildirim, Ph.D.
>> -----------------------------------------------------------
>> = Department of Chemistry - 2145 Sheridan Road =
>> = Northwestern University - Evanston, IL 60208 =
>> = Ryan Hall #4035 (Nano Building) - Ph.: (847)467-4986 =
>> = Website : http://ilyasyildirim.wordpress.com =
>> = ------------------------------------------------------- =
>> = http://www.linkedin.com/in/yildirimilyas =
>> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
>> -----------------------------------------------------------
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 6
>> Date: Sat, 8 Feb 2014 10:34:09 -0700
>> From: Daniel Roe <daniel.r.roe.gmail.com>
>> Subject: Re: [AMBER] Could not find target 281.850000 in any of the
>> replica trajectories
>> To: AMBER Mailing List <amber.ambermd.org>
>> Message-ID:
>> <CAAC0qOYxBm3B+NKGuTfsTFxvJ949kRxjoRFLni6MK7ixzMiVUw.mail.gmail.com>
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi,
>>
>> On Sat, Feb 8, 2014 at 4:39 AM, <sunita.tifrh.res.in> wrote:
>>
>>> PTRAJ: trajin remd_0.4ns.mdcrd.001 remdtraj remdtrajtemp 281.85
>>> Checking coordinates: remd_0.4ns.mdcrd.001
>>> REMDTRAJ: Using specified file as lowest replica: remd_0.4ns.mdcrd.001
>>> REMDTRAJ: Frames at 281.850000 K will be processed.
>>> REMDTRAJ: Scanning for other REMD files.
>>> REMDTRAJ: Found 1 replica traj files.
>>>
>>
>> I think this is your problem. If you want to extract a specific temperature
>> from a replica ensemble you need to have all replica trajectories present
>> so that all temperatures are present. Presumably there are other replica
>> trajectories somewhere named remd_0.4ns.mdcrd.002, remd_0.4ns.mdcrd.003,
>> etc (one for each replica). They should be in the same location as
>> remd_0.4ns.mdcrd.001. This needs to be done for each replica 'trajin'.
>>
>> Hope this helps,
>>
>> -Dan
>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 201
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>>
>>
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>> End of AMBER Digest, Vol 759, Issue 1
>> *************************************
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 8 Feb 2014 22:08:33 -0500
> From: David A Case <case.biomaps.rutgers.edu>
> Subject: Re: [AMBER] AMBER Digest, Vol 759, Issue 1
> To: AMBER Mailing List <amber.ambermd.org>
> Message-ID: <20140209030833.GB40329.biomaps.rutgers.edu>
> Content-Type: text/plain; charset=us-ascii
>
> On Sat, Feb 08, 2014, Arjun Sharma wrote:
>>
>> Thanks for the reply. It usually crashes at the 81st step of 100 step
>> minimization. However, it does work when maxcyc = nyc in minimization
>> script. I am not sure if that is the right way to minimize.
>
> I'm guessing you have water as a solvent, but you have not turned SHAKE
> on. This can lead to failure of the type you see, where the hydrogen atom
> of one water molecule gets too close to the oxygen of another, leading
> to arbitrarily large negative electrostatic energies -- you can see that
> happening in you simulation.
>
> See if turning on SHAKE fixes things.
>
> ...dac
>
>
>
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