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

[gal.fradin at live.biu.ac.il]

dear Xian,
 
open the PDB using text editor and replace the name...
 
good luck
 



From: xianshine at gmail.com
To: gmx-users at gromacs.org
Date: Tue, 13 Sep 2011 15:36:41 +0800
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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