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

[David Mobley]

re: Mark's comment, pdb2gmx doesn't seem to be able to do the atom typing,
etc., necessary to be able to deal with general small molecules. Or if it
can in some cases, at least not the cases in which I've tried it. :) I think
it's geared primarily towards proteins. But Mark is right -- the output from
PDB in .itp format is not all-atom. You can get nominally all-hydrogen mol2
files out but then you still have to have some way of converting these to
gromacs topologies. And it sometimes leaves out hydrogens, too, in my
experience.

On 11/17/05, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
>
> 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
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