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Dear Mark,<br>
Thank you for your kind reply. As you said I have
defined the residues in the .rtp file. When I ran grompp command it
gave me following error:<br>
Fatal error: Bonded/nonbonded atom type 'C3' not found!<br>
<br>
What may be the reason? Do I need to enter the residue some oher file? <br>
<br>
Thanking you in advance. I am stuck please reply me for this.<br>
Waiting for your kind reply.<br>
<br><font face="Arial" size="2"><TABLE STYLE="border-color: blue; border-left: 1px solid blue; padding-left: 5px;"><tbody><TR><TD><b><i>-- Original Message --</i></b><br>From: "Marc F. Lensink" <lensink@scmbb.ulb.ac.be><br>To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>Date: Thu, 18 Aug 2005 11:51:27 +0200<br>Subject: Re: [gmx-users] problem while entering a new residue in ffgmx.rtp file<br><br><br>On Thu, Aug 18, 2005 at 03:09:04PM +0530, Rahul Karyappa wrote:<br>> <br>> Dear all,<br>> <br>> I have a polyethylene.pdb file for 10 repeat units of<br>> polyethylene. I want to define atoms and bonds for residue PE in the<br>> ffgmx.rtp file. When I enter all the atoms as it is in the .pdb file<br>> and define the bonds, I am able to run pdb2gmx. But if I<br>> want to run pdb2gmx on higher no. of repeat units then<br>> it will be time-consuming to define each atom and bond. Can I add atoms<br>> and bonds for one repeat unit<br><br>you have to define 3 'residues' in the .rtp file:<br>* head<br>* section (the repeating unit)<br>* tail<br><br>cheers,<br>marc<br>_______________________________________________<br>gmx-users mailing list<br>gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<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><br>*****************************************************************<br>This email is virus free by TrendMicro Inter Scan Security Suite.<br>*****************************************************************<br></TD></TR></tbody></TABLE></font></BODY></HTML>
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