[gmx-users] how to simulate a protein and a ATP moleculesimultaneity?

Christopher Stiles CS145331 at albany.edu
Thu Aug 9 04:50:05 CEST 2007

Use x2top to build your top file for the ATP, and then used editconf to make
the gro file and then u can use genbox to put the protein and the ATP in the
same box.

Btw I am not 100% on this since I have not done it before but from the vast
amounts of reading I have done this seems like what you should do, also take
a look at the manual and the wiki to find out how to use these apps.


~Christopher Stiles

College of Nanoscale Science and Engineering (CNSE) 

State University of New York, Albany, New York 12203, USA




From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of mjduan at smail.hust.edu.cn
Sent: Wednesday, August 08, 2007 9:51 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] how to simulate a protein and a ATP


Dear GROMACS users:
I want to simulate a complex composed by a protein and an ATP molecule, and
when I use the pdb2gmx to build the topology file and transfer thepdb file
to gro file, it said "Fatal error: Atom PG in residue ATP 1 not found in rtp
entry with 36 atoms while sorting atoms", So how can I build the top file
and gro file for ATP molecular and simulate the protein molcular and ATP
molecule simultaneity?
Best wishes!

Mo-Jie Duan

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