<div>Hi Mark,</div> <div> </div> <div>I have changed the atom name in the co-ordinate file. Now I get an error saying : </div> <div>Residue "pop" not found in residue database</div> <div> </div> <div>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.</div> <div> </div> <div>Thanks,</div> <div>Aj<BR><BR><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>> Thank you for your valuable suggestion.I did go through the manual, but <BR>> I want to confirm if I need to add the atom CA in the ffoplsaa.rtp file, <BR>> and if so I am not sure what the appropiate Type of angles, Type of <BR>> proper dihedrals, Type of improper dihedrals I have to enter.<BR>> If I choose the force field with option 0
then it gives me an error <BR>> saying residue AIB not found in residue topology.<BR><BR>I can't reconcile the above with your original problem. All you need to <BR>do is have a coordinate file whose residue names correspond to those in <BR>your .rtp file, and then atom names that correspond to those in the <BR>residues in the .rtp file.<BR><BR>You should be careful to follow the advice in Step 2 of <BR>http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation and if <BR>appropriate http://wiki.gromacs.org/index.php/Parameterization<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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