[gmx-users] Re: gmx-users Digest, Vol 95, Issue 208

Erik Marklund erikm at xray.bmc.uu.se
Fri Mar 30 16:46:10 CEST 2012 

Everything beyond dssp 2.0 uses a new syntax, which is not (yet) supported in gromacs. The new way of invoking dssp is described on the dssp webpage. Although undocumented, version 2.0 still accepts the old syntax, but NOT the -na flag, which is set by do_dssp unless you ask for syrface area calculations. Try to either install dssp 1.X or add e.g. the -a flag when executing do_dssp. The latter worked to my surprise.

There is a fix for this issue up for review that will (hopefully) go into gromacs 4.6. If you can't wait for that, it's pretty straightforward to modify how dssp is invoked in src/tools/do_dssp.c.

Erik

30 mar 2012 kl. 16.38 skrev Albert:

> 
> 
> I've tried: 2, 2.1.3, 2.1.4, the problem is still there. I don't think the do_dssp is so difficult. just one command:
> 
> do_dssp -s md.tpr -f md.trr -b 100 -e 200 -f ss.xpm
> 
> 
> On 03/30/2012 03:05 PM, Erik Marklund wrote:
>> 
>> And what versions were those?
>> 
>> 30 mar 2012 kl. 15.06 skrev Albert:
>> 
>>> I've tried different kind of DSSP version, but the problem is the same....
>>> 
>>> 
>>> On 03/30/2012 02:54 PM, gmx-users-request at gromacs.org wrote:
>>>> Send gmx-users mailing list submissions to
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>>>> When replying, please edit your Subject line so it is more specific
>>>> than "Re: Contents of gmx-users digest..."
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>>>> 
>>>> Today's Topics:
>>>> 
>>>>    1. Re: Re: do_dssp error (Erik Marklund)
>>>>    2. Re: Not able to continue with Equilibration (Justin A. Lemkul)
>>>>    3. Re: HB lifetime (Nidhi Katyal)
>>>>    4. Re: HB lifetime (Justin A. Lemkul)
>>>> 
>>>> 
>>>> ----------------------------------------------------------------------
>>>> 
>>>> Message: 1
>>>> Date: Fri, 30 Mar 2012 13:28:05 +0200
>>>> From: Erik Marklund<erikm at xray.bmc.uu.se>
>>>> Subject: Re: [gmx-users] Re: do_dssp error
>>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>>>> Message-ID:<129A1E28-ABBD-4733-BA85-C1F6B2F4BE89 at xray.bmc.uu.se>
>>>> Content-Type: text/plain; charset="us-ascii"
>>>> 
>>>> And I replied "What's your dssp version? The most recent ones have different flags that are not yet supported by gromacs."
>>>> 
>>>> Erik
>>>> 
>>>> 30 mar 2012 kl. 13.23 skrev Albert:
>>>> 
>>>>> Hello:
>>>>>  there is some problem for my do_dssp, it always claimed:
>>>>> 
>>>>> Program do_dssp_d, VERSION 4.5.5
>>>>> Source code file: do_dssp.c, line: 572
>>>>> Fatal error:
>>>>> Failed to execute command: /usr/local/bin/dssp -na ddg1g7Id ddRwthIi>  /dev/null 2>  /dev/null
>>>>> 
>>>>> 
>>>>> someone suggest to compile gromacs with double precision and I recompiled it with --enable-double
>>>>> but it still doesn't work.....
>>>>> 
>>>>> does anybody else have any suggestions?
>>>>> 
>>>>> THX
>>>>> -- 
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-request at gromacs.org.
>>>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>> -----------------------------------------------
>>>> Erik Marklund, PhD
>>>> Dept. of Cell and Molecular Biology, Uppsala University.
>>>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>>>> phone:    +46 18 471 6688        fax: +46 18 511 755
>>>> erikm at xray.bmc.uu.se
>>>> http://www2.icm.uu.se/molbio/elflab/index.html
>>>> 
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>>>> ------------------------------
>>>> 
>>>> Message: 2
>>>> Date: Fri, 30 Mar 2012 08:26:05 -0400
>>>> From: "Justin A. Lemkul"<jalemkul at vt.edu>
>>>> Subject: Re: [gmx-users] Not able to continue with Equilibration
>>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>
>>>> Message-ID:<4F75A65D.1040701 at vt.edu>
>>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>> 
>>>> 
>>>> 
>>>> francesca vitalini wrote:
>>>>> Dear Mark,
>>>>> Thank you for your answer. I'm trying now with the position restraints
>>>>> and see what happens.
>>>>> However, another question came up to my mind in the mean time. I'm
>>>>> using GROMACS 3.3.1 (version with mapping for reverse transformation,
>>>>> I have been posting on it before) and for the mdrun the flag -coarse
>>>>> is required. From the mdrun -h help, the -coarse flag resulted to be a
>>>>> generic trajectory, so I assumed it was needed for the names of the
>>>>> atoms or something similar. However, trying to run the nvt.mdp with
>>>>> the original coarse grained file specified for this flag, resulted in
>>>>> the simulation not dying at the very first steps.
>>>>>  I'm not sure if it will work out eventually ( the 20 ps simulations
>>>>> is supposed to finish in 12 hours, which is still kind of worrying
>>>>> despite my system being pretty big) but definitely told me that the
>>>>> -coarse flag might be of fundamental importance.
>>>>> Unfortunately I couldn't find any more detailed documentation about it.
>>>>> Could anyone explain to me what it does or point me to where to find
>>>>> the related documentation?
>>>> Where did you obtain this version of Gromacs?  You're not using an official
>>>> version, so you're not likely to find its documentation in the usual places and
>>>> it's very hard for this community to help you using a modified version of
>>>> antiquated software.  You're more likely to have luck contacting whoever created
>>>> these modifications for help, since potential problems with code stability and
>>>> performance are likely best addressed by those who made the modifications.
>>>> Perhaps they are members of this list, but contacting them directly is probably
>>>> a better approach.
>>>> 
>>>> -Justin
>>>> 
>> 
>> -----------------------------------------------
>> Erik Marklund, PhD
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596,    75124 Uppsala, Sweden
>> phone:    +46 18 471 6688        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se
>> http://www2.icm.uu.se/molbio/elflab/index.html
>> 
> 
> 
> -- 
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
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> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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