[gmx-users] ATP and ADP topologies for the OPLS force field

[Mark Abraham]

TJ Piggot wrote:
> Hi I sent this email a few weeks ago and have had no replies yet I hope 
> that someone will be able to help this time.
> 
> I am trying to construct ATP and ADP topology files for use with the opls
> force field. I have previously been able to do this for the ffG43a1 force
> field using prodrg.
> 
> However prodrg does not produce output files for use with the opls force
> field. I have tried to change the prodrg output files (.itp) for ADP and
> ADP but the problem is that there is not enough atoms as the individual
> hydrogens are not defined.

OPLS/AA is an all-atom force field, whereas the GROMOS force fields are 
not. Perhaps you should review why you are using whatever force field 
you think you should be using. I have no idea what prodrg does, but if 
it writes OPLS/AA-suitable topologies and you want to go along this path 
then you should go ahead and make prodrg do so. Otherwise you need to 
look at alternatives, like generating a PDB structure (with or without 
hydrogens) and, if that structure is without hydrogens, then using some 
tool to generate hydrogens (e.g. gromacs' pdb2gmx?)

Mark