<div>Hi Mark,</div> <div> </div> <div>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?</div> <div> </div> <div>Now when I run grompp I am getting the error </div> <div> </div> <div>"Atomtype 'opls_135' not found!" .............</div> <div> </div> <div>Any suggestions highly appreciated..</div> <div> </div> <div> </div> <div>Thanks,</div> <div>Aj</div> <div> </div> <div> </div> <div><B><I>Mark Abraham <Mark.Abraham@anu.edu.au></I></B> wrote:</div> <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">ASHWINI JAYAPRAKASH wrote:<BR>> Hi Mark,<BR>> <BR>> I have changed the atom name in the co-ordinate file. Now I get an error <BR>> saying :<BR>> Residue "pop" not found in residue database<BR>> <BR>> My co-ordinate file
consists of protein, popc and sol. Do I have to add <BR>> the itp files of popc and sol to the rtp file.<BR><BR>Only if you want pdb2gmx to recognise these types of residues. See <BR>http://wiki.gromacs.org/index.php/topology_file or chapter 5.<BR><BR>Mark<BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> 
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