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