Dear Mark, Thanks for your invaluable advice. I solved my problem.
Samad --- On Thu, 4/24/08, Mark Abraham <[EMAIL PROTECTED]> wrote: > From: Mark Abraham <[EMAIL PROTECTED]> > Subject: Re: [gmx-users] A question > To: "Discussion list for GROMACS users" <[email protected]> > 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 [email protected] > 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 [EMAIL PROTECTED] > 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 _______________________________________________ gmx-users mailing list [email protected] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
