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

David Mobley dmobley at gmail.com
Thu Nov 17 17:23:31 CET 2005

I can't say much about ATP and ADP specifically, but one general piece of
advice I have about topology files for small molecules is that prodrg
doesn't necessarily place all of the hydrogens if they're not initially
present, which inevitably results in problems in some cases. There are a
variety of programs which can protonate molecules, so you might try one of
those. I've also had some success in some cases using OpenEye's "convert" (
http://demo.eyesopen.com/cgi-bin/convert/convert.out), but it doesn't
generate GROMACS topology files. Perhaps someone will have more general

About charges, my sense is that it's probably not wise to use charges from
prodrg. I would probably try to use some package which computes more
sensible quantum mechanical charges which are more similar to those used in
parameterizing force fields. See this note from the FAQ for prodrg:

 Q: The atomic charges don't always come out right?

A: This is a well known limitation. PRODRG works with the concept of charge
groups, which are defined as a group of bonded atoms with an integer charge.
E.g. -COO would have the C (with a slight positive charge) and the two O's
(with an equal negative charge) in one "charge group" with the total charge
being -1. Thus in order for PRODRG to assign atomic charges it needs to be
able to recognise the charge groups first. This is particularly difficult in
ring systems with nitrogens, and several charge group definitions (e.g.
C-Cl) or still missing. I would definitely recommend that you check these
charges before starting your 2 microsecond simulation.

I haven't been using OPLS, myself; I'm actually using the AMBER force field,
but my usual method for setting up topologies is this:
1) Generate a mol2 file of the small molecule, including hydrogens
(sometimes using OpenEye's convert).
2) Use AMBER's antechamber package to calculate AM1-BCC charges and generate
amber topologies, as well as do atom typing.
3) Convert AMBER topologies to GROMACS topologies using the AMBER ff.

This isn't as crazy as it sounds since I'm using the AMBER ff. But others on
the list may have a better procedure for generating topologies directly in
GROMACS. I think your problem is really with step 2-3, and there must be
other packages that can do this easily.


On 11/17/05, TJ Piggot <t.piggot at bristol.ac.uk> 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.
> Can i change this .itp to include the hydrogens and if so what values do i
> need to use for the charges and masses of these new atoms ?
> Also if anyone has already constructed these topology files and could send
> them to me i would be very grateful.
> Thanks in advance
> Tom Piggot
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
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