[gmx-users] A question

samad ahadian samad_ahadian at yahoo.com
Fri Apr 25 02:30:57 CEST 2008

Dear Mark,

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
> tutorials.
> Mark
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php

Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ

More information about the gromacs.org_gmx-users mailing list