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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of [EMAIL PROTECTED] Sent: Wednesday, August 08, 2007 9:51 PM To: gmx-users@gromacs.org Subject: [gmx-users] how to simulate a protein and a ATP moleculesimultaneity? 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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