Re: [AMBER] CHAMBER prmtop

From: Mark Williamson <>
Date: Mon, 27 Jun 2011 19:27:17 +0100

On 27/06/2011 17:41, Manish wrote:
> Hi All,
> I've converted CHARMM psf to AMBER prmtop using CHAMBER. In the prmtop file
> I find that the unit for K_ub is kcal/mole/rad**2. In the CHARMM parameter
> file the unit is kcal/mole/A**2. Could anyone please explain the difference
> in the units and also how to interconvert between the two.

Dear Manish,

The Urey Bradley force field term is harmonic and is a function of,
purely, the distance between the 1,3 atoms bonded by a common atom.

When I was working on CHAMBER, I made use of an unused feature in the
prmtop format (, that is, the
%COMMENT flag. Here I placed extra information about each term, to aid
anyone who might be reading the file, e.g.

%COMMENT K_ub: kcal/mole/rad**2

So, looking at this, you are indeed correct, there is an error in the
units of the comment since this is a function of distance and not an
angle. Seeing that this is an comment typo, it will have no effect on
the actual calculation. I have corrected this in the development tree.
Thank you for the report.

> Another question is that the prmtop top created above has UB term in the
> form i,k,index. Is there a way I can get the list of UB terms as three atoms
> (I,j,k) form using this prmtop.

The position of atom j in evaluating the potential energy and force is
redundant, hence I saw no need carry this value over.

My testing of the implementation focused on ensuring that for a given
system, with a specific CHARMM topology and set of coordinates, I was
able to obtain the same potential energy decomposition across the terms
and the same forces on each atom, (within machine precision) with both
the charmm executable and SANDER/PMEMD. There are examples of this in
the AmberTools/test/chamber/dev_tests .

You might be able to edit the CHAMBER code and the corresponding parsing
routines in SANDER/PMEMD if you wanted to keep the information of j. If
this information is desperately needed, perhaps we could try to work
something out, but I fear introducing this now may break backward



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Received on Mon Jun 27 2011 - 11:30:03 PDT
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