[gmx-users] Re: Add acetyl and amide caps to a peptide with pdb2gmx

[Stephane Abel]

Hi Justin,


I have resolved problem: A typo for the NH2 cap dihedral parameters in 
ff53a6.rtp file  (as you indicate in your tutorial).


Thank you


Stef. 


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> Today's Topics:
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>    1. Re: g_wham error (Justin A. Lemkul)
>    2. Re: How to edit the cgnr and charge fields of a ITP file	with
>       the result of Gaussian? (Justin A. Lemkul)
>    3. Re: How to edit the cgnr and charge fields of a ITP, file
>       with the result of Gaussian? (Thomas Schlesier)
>    4. Re: Add acetyl and  amide caps to a peptide with pdb2gmx
>       (Justin A. Lemkul)
>    5. Re: How to edit the cgnr and charge fields of a ITP file	with
>       the result of Gaussian? (Mark Abraham)
>    6. Re: density and intramolecular interactions (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 11 Sep 2009 06:19:13 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] g_wham error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4AAA2421.8020805 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
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>
>
> Ragnarok sdf wrote:
>   
>> While trying to analyse my several windows with g_wham the following error
>> appears :
>>
>> Fatal error:
>> Pull geometry direction not supported
>>
>> my entry files consist on the several px.xvg listed in a .dat entry file and
>> the several .tpr from each of the simulations also listed in a tpr.dat file
>>
>>     
>
> Right, but error is coming from the .tpr files, themselves, sort of. 
> Unfortunately g_wham only works when you've specified "pull_geometry = distance" 
> in the .mdp file.  Maybe this should be documented somewhere?  g_wham -h does 
> not make this clear.
>
> -Justin
>
>   
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