Re: AMBER: Identification of improper torsions in small molecules parameterized with GAFF by antechamber

From: John Chodera <>
Date: Tue, 28 Oct 2008 08:57:42 -0700


Many thanks for the extremely helpful reply!

I think "pretty rare" is a good assessment -- David Mobley mentioned
that he had to add two improper parameters for nitros when he
parameterized a set of 504 neutral small molecules for hydration free
energy calculations in [1], and another improper parameter for the set
of ugly compounds in the CUP SAMPL hydration free energy challenge set
in [2]:

ca-o-no-o 1.1 180. 2. DLM addition, 7/2007, following above; some nitros
c3-o-no-o 1.1 180. 2. DLM addition, 10/2007, following above, for nitros
o-o-no-os 1.1 180. 2. DLM addition 1/2008 for compounds in CUP set, as above

The suggestion of just processing the LEaP-generated prmtop is a good
one -- I'll see if I can make that work.

With some luck, we'll be able to put together a tool capable of
transforming Amber crd/prmtop files to and from the Maestro format
Desmond uses. This could be useful to Amber users interested in
having more options in setting up or running their simulations. The
Maestro GUI that comes with the free Desmond academic distribution
might be easier for some users, and the connectivity-based parameter
assignment of the Desmond parameter assignment tool could be
tremendously useful in some pathological atom-name-mangling




[1] D. L. Mobley, J. D. Chodera, and K. A. Dill. "Entropy and
conformational change in implicit solvent simulations of small
molecules", J. Phys. Chem. B 112:938-946 (2008).

[2] D. L. Mobley, C. I. Bayly, M. D. Cooper, M. R. Shirts, and K. A.
Dill. "Small molecule hydration free energies in explicit solvent: An
extensive test of fixed-charge force fields", submitted, J. Phys.
Chem. B. Inquire for preprint.

John D. Chodera
QB3-Berkeley Fellow, University of California, Berkeley
mobile: 415.867.7384
2008/10/28 David A. Case <>:
> On Mon, Oct 27, 2008, John Chodera wrote:
>> I have a question about how precisely improper torsions that are to be
>> applied to small molecules that have been parmeterized for GAFF by
>> antechamber are generated.
>> As far as I can tell, there are at least THREE programs that identify
>> all of the improper torsions in the AmberTools distribution:
>> * prepgen
>> * parmchk
>> * leap
>> The codebases for these three programs are entirely separate, and the
>> algorithms they use for identifying impropers appear to all be
>> different.
>> LEaP appears to have the 'final word', in that it actually searches
>> for torsion parameters to apply.
> This is correct: leap makes the torsions that are actually used in the energy
> evaluations.  (I think prepgen is irrelevant here: any torsions in a prep file
> are ignored by leap anyway [except for some debug printout].  We are trying to
> wean people away from using prep-format files, in favor of mol2-format.)
>> There are anecdotal reports (on the
>> mailing list) of users finding that parmchk fails to generate all the
>> parameters expected by LEaP, which will still complain about missing
>> impropers until they are added to the gaff.dat file.
> I think this is pretty rare(?).  Junmei has reported that some very large
> percentage of the NCI small molecules get all of the values they need from
> either gaff.dat or parmchk.  The virtual screening in DOCK (using amberscore)
> also uses this route -- people on the list may be able to comment on how often
> this really occurs.
>> In converting small molecules over to Desmond, I need to identify all
>> of the improper torsion angles in the small molecule.  Would running
>> 'prepgen' (or some other antechamber-based tool) be sufficient to do
>> this, or should I run leap and examine the output if I want to
>> generate something that will be exactly the same as what would be
>> generated for Amber?
> Safest is to run leap and examine the resulting prmtop file; the rdparm
> program formats prmtop info in a little nicer fashion.
> ...good luck...dac
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Received on Wed Oct 29 2008 - 05:10:47 PDT
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