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
On Feb 8, 2014, at 2:00 PM, amber-request.ambermd.org wrote:
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> AMBER Mailing List Digest
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> 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)
>
>
> ------------------------------
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> End of AMBER Digest, Vol 759, Issue 1
> *************************************
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Received on Sat Feb 08 2014 - 15:30:03 PST
