[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[mjduan]

Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.top file) only contain the atoms of the protein and water.)
And is there any difference between the .mdp file to do grompp for this complex and for the system only contain protein and water?

mjduan at smail.hust.edu.cn wrote:
> 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 
> the*pdb* 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?

By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.

Mark

_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php