[gmx-users] how to handle different atom names between pdb and rtp files.

KONG Xian xianshine at gmail.com
Tue Sep 13 09:36:41 CEST 2011

Hello, I've got a pdb file,but while I convert it to gro files, I met such


Atom HA in residue MET 1 was not found in rtp entry MET with 11 atoms while
sorting atoms


I find that in the rtp files of the ff files, the H atom linked with C-alpha
is called H, but in the pdb file, the same hydrogen atom is called HA, I
think this may be the problem. 


So, my problem is, how to convert my pdb files to make the atom names
consistent between the pdb and rtp files?




Tsinghua University, Beijing, China


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