Hi Mark, I have used pdb2gmx to create the topology file with the option of -missing,also I have deleted the HEATOM that were there in the pdb file. Will these be a problem later? Now when I run grompp I am getting the error "Atomtype 'opls_135' not found!" ............. Any suggestions highly appreciated.. Thanks, Aj Mark Abraham <[EMAIL PROTECTED]> wrote: ASHWINI JAYAPRAKASH wrote: > Hi Mark, > > I have changed the atom name in the co-ordinate file. Now I get an error > saying : > Residue "pop" not found in residue database > > My co-ordinate file consists of protein, popc and sol. Do I have to add > the itp files of popc and sol to the rtp file.
Only if you want pdb2gmx to recognise these types of residues. See http://wiki.gromacs.org/index.php/topology_file or chapter 5. Mark _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php --------------------------------- Ready for the edge of your seat? Check out tonight's top picks on Yahoo! TV.
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