[gmx-users] ATP and Gromacs
kamilt at ibmb.uni.wroc.pl
Mon Apr 26 19:50:01 CEST 2004
Well I've made a mistake and responded to the wrong message.
Here is a small tip:
Please check your input file (ATP section) and compare it with ffgmx.rtp topology file. It seems that You will have to change the name of Your ATP atom PG to the name listed in ffgmx.rtp. If You are not succesfull please try to reconstuct Your topology by calculationg a new one . You can do it with http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html ProdG server.
As for the hydrolysis, You will not be able to simulate the phenomenum of ATP hydrolysis unless You use the quantum approach. A typical MD can't simulate covalent bond formation.
----- Original Message -----
From: SLN Prasad Reddy
To: gmx-users at gromacs.org
Sent: Monday, April 26, 2004 7:36 PM
Subject: [gmx-users] ATP and Gromacs
I am trying to run gromacs on a protein having ATP.I started simulation with a command "pdb2gmx" and it is giving following error
Fatal error: Atom PG in residue ATP 250 not found in rtp database
while sorting atoms
Please suggest me how to overcome this.
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