Hi Thanks, I thought so too.
My command line is: pdb2gmx -f xxx.pdb file The -ter flag is set to default, i.e. charged termini. When I use the -ter flag for interactive termini selection and I select NONE for both N- and C-ter the message becomes: Program pdb2gmx, VERSION 4.0.99-dev-2010-07-07 08:35:28 -0700-7cbc3b9-dirty Source code file: pdb2top.c, line: 887 Fatal error: There is a dangling bond at at least one of the terminal ends. Select a proper terminal entry. For more information and tips for troubleshooting, please check the GROMACS Best George ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Friday, July 09, 2010 8:08 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] pdb2gmx with DNA Patargias, George wrote: > Thanks for your reply Justin. > > I am trying to generate a topology dor a dna structure using the charmm > dna.rtp > > I have renamed the residue name to DA , DG etc. I have also set DA5 and DC3 > for > the 5' and 3' ends > > I got this error > > > Fatal error: > atom N not found in buiding block 2DG while combining tdb and rtp > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > I quess I need to change something in the .rtp and/or the .tdb files. But > what? > Maybe, maybe not. It looks like pdb2gmx is trying to treat your DNA as protein. What is your command line? What are you choosing for termini? -Justin > Thanks a lot > > George-- > 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 MILES-IGERT Trainee 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 -- 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
