On 19/07/2011 11:56 PM, sa wrote:
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
<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-CP10.100.0-3.Dimethyl phosphate
1-0.500.0-2.
10.100.01
Where only a positive value makes sense, sometimes people use negative
values to indicate some special functional form. This can be easier to
code. Regardless, you'll have to check out the GLYCAM documentation and
see what is meant, before you can address how to convert it into a
GROMACS format. Obviously the contents of parts of chapter 4 and 5 of
the manual will be important.
Mark
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