Could anyone give me the proper procedure for adding a residue? (Using itp)
________________________________ From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Thu 8/13/2009 1:51 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Adding a residue Smith, Chanel Chonda wrote: > Hello, > I am currently using GROMACS 4. When trying to process the pdb file > with pdb2gmx, an error message came up stating that a particular residue was > not recognized by the residue topology database. I then tried to adding a > molecule in the ff....rtp file and adding the name in aminoacids.dat. This > did not work either. The residue that I need to add is a nonprotein. Could > you tell me how I can add this residue to the database and therefore allowing > me to process the pdb file? > You've followed the correct procedure. If the new residue is a ligand of some sort, it may just be easier to create an .itp file for it (using one of the user-contributed programs, or something like PRODRG). If you still want to use the .rtp approach, provide more details, like the actual .rtp entry and the exact error message that you're getting from pdb2gmx. -Justin > > Thanks, > Chanel King > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
<<winmail.dat>>
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
