The combining rules are applied in tleap, and that only supports the
canonical Amber combining rules, to my knowledge, although I believe that
the OPLS parameter database include with Amber has been adjusted for the
difference in how OPLS and Amber handles sigma. Therefore, you should take
care when breaking from how Amber sets up the prmtop files.
That said, you can accomplish this in ParmEd, although it is not
particularly pleasant. The following script will change the default
combining rules (save it to a file named "combine.pmd"):
===begin combine.pmd===
!!
def combine_rmin(r1, r2):
return (r1 * r2) ** 0.5
type(amber_prmtop.parm).combine_rmin = combine_rmin
!!
===end combine.pmd===
Then, you can source this combine.pmd file in any parmed.py session (make
sure you launch parmed.py with the "-e" flag to enable the built-in Python
interpreter). Then you can use the command (including the !):
!amber_prmtop.parm.recalculate_LJ()
inside ParmEd to forcibly recompute all of the standard LJ terms according
to your new combining rules.
HTH,
Jason
P.S. As a programming alternative, if you are comfortable with Python, you
can use the chemistry.amber.readparm.AmberParm class directly in one of
your own scripts (you will need to override the AmberParm.combine_rmin
method to the combining rule of your choosing). You can go to
$AMBERHOME/AmberTools/src/parmed and run the command "make docs" to create
a bunch of doxygen PDF and HTML docs describing the various classes and
their methods. (Or, of course, import the classes you want into an
interactive Python shell and use the help() function to print effectively
the same information). The AmberTools manual also has some information
about the AmberParm class (look for the ParmEd chapter).
On Thu, Aug 22, 2013 at 7:53 PM, X Sun <egeh00.aol.com> wrote:
> Dear all,
>
> My problem is using Amber with OPLS-AA force field. For the ó in the Van
> der Waals parameters, Amber uses óij=0.5*(óii+ ójj), OPLS-AA uses óij=
> (óii*ójj)^0.5. Is there any option in Amber to set up the method to get a
> geometrical average for ó ?
>
> Xiaoquan Sun.
>
> 2013-08-22
>
>
>
> X Sun
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 22 2013 - 19:30:04 PDT
