[gmx-users] ATP and Gromacs

Kamil Tamiola 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. 

Good Luck 

  ----- 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

  Hi ,
        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. 

  Thank you

  Prasad reddy 

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