Remove all the hydrogens from the pdb file and then try to run pdb2gmx, I hope it'll do fine. Or you can also use -ignh option as suggested by Justin.
Tarak On Fri, May 10, 2013 at 3:35 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 5/10/13 5:16 AM, Jernej Zidar wrote: > >> Hi, >> In CHARMM I generated a short peptide. The N-terminal is a regular >> -NH2 (patch NNEU) while the C-terminal is amidated (patch CT2). >> >> I would like to import the PDB to GROMACS using pdb2gmx by using the >> CHARMM27 forcefield later. I issue the following command: >> pdb2gmx -v -f irik-l.pdb -inter >> >> and choose the appropriate protonation states of the aminoacids, the >> N-/C- terminal patches, solvent but the import fails: >> Program pdb2gmx, VERSION 4.6 >> Source code file: /home/zidar/utils/gromacs-4.6/**src/kernel/pdb2gmx.c, >> line: 727 >> >> Fatal error: >> Atom H1 in residue ILE 1 was not found in rtp entry ILE with 20 atoms >> while sorting atoms. >> >> For a hydrogen, this can be a different protonation state, or it >> might have had a different number in the PDB file and was rebuilt >> (it might for instance have been H3, and we only expected H1 & H2). >> Note that hydrogens might have been added to the entry for the N-terminus. >> Remove this hydrogen or choose a different protonation state to solve it. >> Option -ignh will ignore all hydrogens in the input. >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at >> http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors> >> - - - - >> >> Atom H1 (and H2) is the atom from the both the N-/C- terminals that >> in CHARMM is part of the residue ILE but Gromacs (4.6.1) does not >> recognize it properly as they are renamed: >> Renaming atom 'HT1' in residue 1 ILE to 'H1' >> Renaming atom 'HT2' in residue 1 ILE to 'H2' >> >> How can one solve this problem? >> >> > Have you tried -ignh like the error output suggests? > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<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<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> > -- 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