Hi all, I am trying to use AMBER ff in GROMACS. I have followed the steps that are given in the http://chemistry.csulb.edu/ffamber/ link.
The first residue of the protein is GLN. I put an N prefix to this residue. The pdg2gmx works well except giving an warning of long bond between some atoms. In contrast, if I have not put any prefix to GLN, then, the following error appears: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ WARNING: atom H is missing in residue GLN 1 in the pdb file You might need to add atom H to the hydrogen database of residue GLN in the file ff???.hdb (see the manual) ------------------------------------------------------- Program pdb2gmx, VERSION 3.3.1 Source code file: pdb2top.c, line: 697 Fatal error: There were 1 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ I looked at both the .rtp and .hdb files, but everything seems to be correct. Does anybody face with a similar problem? Thanks in advance Ozge Engin ================================= Computational Science & Engineering Koc University _______________________________________________ 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
