AMBER Archive (2008)

Subject: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber

From: Ross Walker (
Date: Wed Nov 26 2008 - 11:28:51 CST

Hi Jeffrey,

> CT-CT-N -C 1 0.50 180.0 -4. phi,psi,parm94
> CT-CT-N -C 1 0.15 180.0 -3. phi,psi,parm94
> CT-CT-N -C 1 0.00 0.0 -2.
> JCC,7,(1986),230
> CT-CT-N -C 1 0.53 0.0 1. phi,psi,parm94

> As stated in JACS1995v117p5179 "The periodicity of the torsion. A negative
> value is not used in the calculation but signifies more than one component
> around a given bond." I don't know what is the role of the parameters in
> line with negative periodicity. I am trying to find the corresponding code
> in src/ but failed to understand so many formal parameters in the
> subroutines...

This has to do with telling leap that it should look for additional torsion
terms for a given set of atom types. From

PN The periodicity of the torsional barrier.
                    NOTE: If PN .lt. 0.0 then the torsional potential
                          is assumed to have more than one term, and the
                          values of the rest of the terms are read from the
                          next cards until a positive PN is encountered.
                          negative value of pn is used only for identifying
                          the existence of the next term and only the
                          absolute value of PN is kept.

I'm not entirely sure if leap strictly follows this though (I believe that
it might just look for all dihedral entry types and this really only
mattered in the days before leap but I might be wrong - a simple test would
be to check).

> The parameterized torsional constants for sulfonium group are:
> -----
> Torsional Interaction (Kcal/mol)
> V1/2 V2/2 V3/2
> SP 每 CT 每 CT 每 CT -1.6814 1.0698 -0.0001
> SP 每 CT 每 CT 每 H1 0.9529 1.1047 0.0695
> SP 每 CT 每 CT 每 O3 3.5661 0.5502 -0.0208
> ----------
> Any one who can give me some suggestions on how to use these parameters in
> AMBER10?

In this case you have 3 torsion terms, I assume corresponding to a 1 fold, 2
fold and 3 fold term. The /2 here corresponds to the Vn/2 yes? I believe
AMBER expects Vn/2 to be specified in the frcmod file and not Vn given the

                           (PK/IDIVF) * (1 + cos(PN*phi - PHASE))

         PK The barrier height divided by a factor of 2.

So assuming the phase is zero you should probably write your frcmod file as

SP 每 CT 每 CT 每 CT 1 -0.0001 0.0 -3
SP 每 CT 每 CT 每 CT 1 1.0698 0.0 -2
SP 每 CT 每 CT 每 CT 1 -1.6814 0.0 1
SP 每 CT 每 CT 每 H1 1 0.0695 0.0 -3


To double check things though I would encourage you to make a prmtop
containing just your sulfonium group. Then load this into rdparm and issues
printdihedrals. This will give you a list of all the dihedrals so you can
manually check that they are all present.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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