You can either use -ighn option in pdb2gmx or mannualy rename the atom names in the pdb file.
Cheers, Jianguo ________________________________ From: KONG Xian <xiansh...@gmail.com> To: gmx-users@gromacs.org Sent: Tuesday, 13 September 2011 15:36:41 Subject: [gmx-users] how to handle different atom names between pdb and rtp files. Hello, I’ve got a pdb file,but while I convert it to gro files, I met such problem: 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? KONG Xian Tsinghua University, Beijing, China 2011/9/13 __________ Information from ESET NOD32 Antivirus, version of virus signature database 6458 (20110912) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com
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