[gmx-users] Conversion of the GLYCAM dihedral parameters in the GROMACS format.

[sa]

Dear GROMCS users,



I am trying to convert some GLYCAM parameters in GROMACS format. For this
purpose, I am using the latest GLYCAM parameters downloaded from the RJ.
Woods’ website and the examples given in the acpype code (here for the
dihedral angles) :


http://code.google.com/p/acpype/source/browse/trunk/acpypi.py?spec=svn9&r=9&redir=1


-------------------
# dihedral    idivf        barrier hight/2 kcal/mol  phase degrees
  periodicity     comments

 X -ca-ca-X    4           14.500*                     180.000
       2.000             intrpol.bsd.on C6H6
* to convert to gmx: 14.5/4 * 4.184 * 2 (?) (yes in amb2gmx, no in
topolbuild, why?) = 30.334 or 15.167 kJ/mol
# X -CA-CA-X    4   14.50        180.0             2.
intrpol.bsd.on C6H6 (from parm99.dat)
# X-CA-CA-X     3    30.33400     0.00000   -30.33400     0.00000
0.00000     0.00000   ; intrpol.bsd.on C6H6

-----------



I have no problems with the parameters for proteins. But, in case of
the GLYCAM parameters, I am a little confused
about the conversion of dihedral force constants (DFC), especially
when the DFC and the periodicity values are < 0 for example
for this torsion:

O2-P -OS-CP   1    0.10          0.0            -3.         Dimethyl
phosphate

              1   -0.50          0.0            -2.

              1    0.10          0.0             1



Thank you in advance, for your help



SA
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