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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 9 04:50:42 CEST 2007

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.


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