[gmx-users] ATP and Gromacs

[Nuno R. L. Ferreira]

Back to my "old" good days, while a biochemist student.
A resting human consumes about 40 Kg of ATP in 24 hours.
During heavy exercises, it could reach 0.5 Kg /minute.

Regards.
Nuno
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Nuno Ricardo Santos Loureiro da Silva Ferreira
Departamento de Química
Faculdade de Ciências e Tecnologia
Universidade de Coimbra
3004-535 Coimbra - Portugal
Fax: +351 239 827703  - www.biolchem.qui.uc.pt
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  ----- Original Message ----- 
  From: Kamil Tamiola 
  To: gmx-users at gromacs.org 
  Sent: Monday, April 26, 2004 6:45 PM
  Subject: Re: [gmx-users] ATP and Gromacs


  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 

  Kamil
    ----- 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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