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

[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:
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> Today's Topics:
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>     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
>> -- 
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> -----------------------------------------------
> 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>
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>
>
> 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
>