When a CA HETATM record goes through pdb2gmx in the resulting .gro file it is still called "CA", even though in ffG43a1.rtp the matching residue is CA2+. Furthermore, in the itp file it says:
type res atom 1 CA2+ 1 CA CA ... (FORM A) whereas for something like CYS2 it says: 1 CH2 9 CYS2 CB ... So my question is, what is the rule supposed to be for renaming residues? My modified program renames amino acid residues in the res column exactly like the original pdb2gmx but for CA it comes up with: 1 CA2+ 1 CA2+ CA ... (FORM B) which is different from the original program. Are the rules supposed to be different for ions or is this a case where the end user was supposed to manually rename CA to CA2+? The original program does issue a warning (twice actually, which is odd since there's only one HETATM line, although there is also a HET line right after FTNOTE), which is: Warning: 'CA' not found in residue topology database, trying to use 'CA2+'. And it does use it - sort of. In other words, all else being equal would it be better if pdb2gmx emitted the relevant line like FORM B or FORM A, above? Thanks, David Mathog [EMAIL PROTECTED] Manager, Sequence Analysis Facility, Biology Division, Caltech _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
