[gmx-users] A question
samad_ahadian at yahoo.com
Fri Apr 25 02:30:57 CEST 2008
Thanks for your invaluable advice. I solved my problem.
--- On Thu, 4/24/08, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] A question
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Date: Thursday, April 24, 2008, 12:37 AM
> samad ahadian wrote:
> > Hello,
> > I am new user of Gromacs. I did a pdb2gmx command on
> my pdb file. I got an error below:
> > "Residue 'XXX' not found in residue
> topology database"
> > I know that I blindly made my pdb file using Materials
> Studio 4.2. Let me know there is a special software to make
> a pdb file? Thank you in advance for your response.
> No, but you can certainly make life hard for yourself by
> using poor
> PDB-producing software, or using good software poorly. See
> http://wiki.gromacs.org/index.php/Errors for some
> background for this
> error. You need to generate a structure file whose residues
> and atoms
> are defined for the force field you intend to use, and
> which are named
> suitably so that pdb2gmx can recognize them. 'XXX'
> suggests that either
> MS4.2, or your usage of it, or both, are making life hard.
> Depending on your level of newness, you should definitely
> do some
> background textbook/manual/literature reading, and/or
> gmx-users mailing list gmx-users at gromacs.org
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