[gmx-users] how to handle different atom names between pdb and rtp files.
ljggmx at yahoo.com.sg
Tue Sep 13 11:22:14 CEST 2011
You can either use -ighn option in pdb2gmx or mannualy rename the atom names in
the pdb file.
From: KONG Xian <xianshine at gmail.com>
To: gmx-users at gromacs.org
Sent: Tuesday, 13 September 2011 15:36:41
Subject: [gmx-users] how to handle different atom names between pdb and rtp
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
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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