[gmx-users] error in running pdb2gmx command

[Mark Abraham]

On 30/06/2011 1:48 PM, rashi parihar wrote:
> thanx @justin..I have seen gromacs web site before posting..the 
> solution of my problem was written in gromacs website was "the atom 
> names are expected to match those found in the .rtp file 
> <http://www.gromacs.org/Documentation/File_Formats/.rtp_File> that 
> define the building block(s) in your structure". Now my question is 
> that how can i see or open the .rtp file of particular force field?

Yes, it's somewhere under share/top of your GROMACS installation 
directory - and probably pdb2gmx prints which one it is trying to use.

Mark

>
> On Wed, Jun 29, 2011 at 5:24 PM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
>     rashi parihar wrote:
>
>
>         HI all ..while running pdb2gmx command .I am getting error
>         "Fatal error:
>         Atom CT in residue TYR 314 was not found in rtp entry TYR with
>         20 atoms
>         while sorting atoms" .what this error mean and how can I
>         rectify this problem?plz help me.
>
>
>     Please search the mailing list archive and Gromacs website before
>     posting. Nearly all common errors are explained on the website or
>     within a few seconds of searching.  For instance:
>
>     http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry
>
>     -Justin
>
>
>         -- 
>          images[12]
>          “Many Smiles Begin Because Of Another Smile . . . ."
>          Regards,
>         Rashi
>
>
>     -- 
>     ========================================
>
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>     ========================================
>     -- 
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>
>
> -- 
> images[12]
> “Many Smiles Begin Because Of Another Smile . . . ."
>
> Regards,
> Rashi
>

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