Hi Carmen, You really have to be careful to match the .rtp to the .pdb building block. pdb2gmx indicates that there's an atom in the .pdb file, which is not found in the [ CHIT ] entry in the .rtp file. If you want better help, you'll have to ask a better question: you should provide more details regarding the CHIT residue in the .pdb file and the (relevant part of) the entry in the .rtp file (in this case the [ atoms ] section).
Cheers, Tsjerk On Wed, Jun 18, 2008 at 7:29 PM, <[EMAIL PROTECTED]> wrote: > I added a new sugar residue in ffG53a6.rtp file, and I included in the > aminaocid.dat file. I got the following problem using pdb2gmx : > ................................................................... > Program pdb2gmx, VERSION 3.3.2 > Source code file: pdb2gmx.c, line: 421 > > Fatal error: > Atom O in residue CHIT 1 not found in rtp entry with 14 atoms > while sorting atoms > ..................................................................... > > I solved the problem temporarily changing the name of my new sugar residue > to "GLCB", that already existed in the ffG53a6.rtp file. > The question is: How should we do this process with more generality? Are > there another file which should be modified or edited? > Thanks a lot > Carmen Esteban > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
