Hey Sajad, That sounds quite serious, having a fetal error (http://www.thefreedictionary.com/fetal)!
But it seems you just have a missing atom, as is indicated in the output. Check the structure before trying to convert it. In particular, read the sections in the PDB file starting with 'REMARK 465' and 'REMARK 470'. Surely you'd also been able to find this in the FAQ or in the archives. Please search there before posting. Hope it helps, Tsjerk On Mon, Apr 18, 2011 at 10:27 AM, Sajad Ahrari <sajadahr...@yahoo.com> wrote: > dear users > after running the command "pdb2gmx -f 1OL5.pdb -o 1OL5.gro -water spc" ,i > was faced with the erorr: "Fatal error: Atom CG not found in residue seq.nr. > 251 while adding atom". i used Gromacs 4.5.3 > with AMBER99SB force field. it seems that some atomes are missing.should i > be modeling the protein to have all it's atoms? is Gromacs have any features > to correct the missing ones? > thanks! > > -- > 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/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
