[gmx-users] ATP and ADP topologies for the OPLS force field
Mark.Abraham at anu.edu.au
Thu Nov 17 17:12:33 CET 2005
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?)
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