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

[Jianguo Li]

You can either use -ighn option in pdb2gmx or mannualy rename the atom names in 
the pdb file.

Cheers,
Jianguo 




________________________________
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 
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

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