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 - - - - 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? Thanks in advance, Jernej -- 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
