On Fri, 18 Feb 2005, Josh Tasman wrote:
I'm getting errors on reading PDB files containin hydrogens added by TRIPOS SYBYL. For example, the atoms 1677-1679 are parsed as Mercury (HG):
ATOM 1674 HD11 ILE A 107 4.939 -2.338 17.094 1.00 0.00 ATOM 1675 HD12 ILE A 107 6.613 -2.979 16.971 1.00 0.00 ATOM 1676 HD13 ILE A 107 5.703 -3.133 18.512 1.00 0.00 ATOM 1677 HG21 ILE A 107 4.770 -2.095 20.141 1.00 0.00 ATOM 1678 HG22 ILE A 107 6.235 -1.314 20.827 1.00 0.00 ATOM 1679 HG23 ILE A 107 4.630 -0.527 21.006 1.00 0.00 ATOM 1680 H ILE A 107 5.291 0.799 16.773 1.00 0.00 ATOM 1681 N TYR A 108 3.267 1.810 19.498 1.00 21.63
Accoring to the table at
http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl There are descrepencies between PDB-like file formats, and we see that the official PDB format would specify "1HG2" instead of "HG21".
Does anyone know of a quick way to deal with this?
I can write a perl search/replace script if need be.
We'll take the suggestion under advisement. Please file a bug report with TRIPOS. We'd be especially happy if they fixed the names, but it would also help if they put the atomic element symbol in columns 77-78 as allowed by PDB version 2. A perl script is an excellent workaround. Regards, Greg