Hi,
Thank you for your reply. I have checked OPLS force field data in Gromacs and AMBER and their sigma values are the same. For example, the first three atom types in gromacs/top/oplsaa.ff/ffnonbonded.itp file is as following:
[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name bond_type mass charge ptype sigma epsilon
opls_001 C 6 12.01100 0.500 A 3.75000e-01 4.39320e-01 ; SIG
opls_002 O 8 15.99940 -0.500 A 2.96000e-01 8.78640e-01 ; SIG
opls_003 N 7 14.00670 -0.570 A 3.25000e-01 7.11280e-01 ; SIG
and in amber/11/dat/leap/parm/opls.info
TYP AN AT CHARGE SIGMA EPSILON
1 06 C 0.500 3.750 0.105 Types 1 - 65 are for proteins from
2 08 O -0.500 2.960 0.210 W. L. Jorgensen & J. Tirado-Rives,
3 07 N -0.570 3.250 0.170 J. Am. Chem. Soc., 110, 1657 (l988).
Their sigma values are the same (the unit in Gromacs and amber is nm and angstrom, respectively). The epsilon values in Gromacs are 4.184 times larger than those in Amber, since the unit in the former is kJ and the unit in the latter is kcal/mol.
So I am wondering how to convert the OPLS nonbonded paramters for use with Amber. Thank you very much.
Sincerely,
Guoxiong
----- Original Message -----
From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thursday, December 15, 2011 3:49 pm
Subject: Re: [AMBER] What's the combine rules for OPLS force field in AMBER?
To: amber.ambermd.org
> I believe OPLS n-b params would have to be converted for use with
> Amber. If you look at the force field formats, you'll see that
> there is nothing to denote whether a nonbond term is OPLS and thus
> should have different combining rules.
>
> Bill
>
> > I am trying to apply OPLS force field in AMBER to simulate a
> box with benzonitrile molecules. I knew that the combine rules
> of AMBER are as following:
> > Epsilon (well-depth) is the geometric mean of the two input
> values. r* (distance at the minimum) is the sum of the two input
> values.>
> > I am wondering what the combine rules for OPLS force field is
> in AMBER. Because in OPLS force field, epsilon and r are both
> geometric mean of the two input values. If amber still uses its
> original combine rules for OPLS force field, it will generate
> wrong parameters for the benzonitrile molecules. If amber still
> uses its original combine rules for OPLS force field, how to
> convert the parameters from OPLS force field to Amber force
> field, i.e. add modifications in frcmod file?
> >
> > Could anyone help me about this problem? Thanks in advance.
>
>
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Guoxiong Su
Cheung Group
Department of Physics
University of Houston
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Received on Thu Dec 15 2011 - 14:30:05 PST
