Hi Brian,
To fully implement the CHARMM force-field in AMBER, you need more than
AMBER-style topologies/parameters (e.g. Urey-Bradley and CMAP parameters
also need to be present). To do this, there is the CHAMBER program, see
section 2.13 in the AmberTools manual.
CHAMBER is great for using the 'real' charmm force-fields in AMBER, but in
my opinion not what you are looking for.
This is mostly because you'd need to use charmm to create .psf files of your
systems and then convert those (plus charmm crd file or pdb file) to prmtop
(plus inpcrd). The resulting prmtop has several differences of a 'normal'
amber prmtop, to incorporate the differences between the force-fields.
Although it may not sound appealing, I think it would be less hassle to do
as you suggest, i.e. make your own files for the limited number of atom
types that you need.
This is only for your specific purpose of course (i.e. testing the influence
of VdW parameters on a system with QM solute & MM solvent). IMO it would be
more tractable to do this all with a 'modified' set of amber-style parameter
files.
Others may chime in with their opinions of course!
Good luck,
Marc
On 20 July 2011 15:09, Brian Radak <radak004.umn.edu> wrote:
> The AMBER11 manual states quite clearly that the CHARMM force field is
> supported in AMBER. However, are there readily available leaprc, frcmod,
> etc. files available for this purpose?
>
> My actual problem is that I would like to compare the differing "solvation"
> properties of the Lennard-Jones sets when the solute (small RNA-like
> molecules) is treated purely by a quantum mechanical method. Thus I have
> no
> real need or desire for bonded terms or even point charges. Am I best off
> just making my own files for the limited number of atom types that I need?
> Unfortunately, anyone who has looked at the mess that is CHARMM27 would
> realize that this requires at least twice as many types as FF99/FF10 and I
> am therefore not particularly excited about doing it.
>
> Any suggestions (besides not using CHARMM) would be appreciated.
>
> Thanks,
> Brian
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Wright-Rieman Hall 101
> Graduate Program in Chemical Physics : 610 Taylor Road,
> Department of Chemistry : Piscataway, NJ
> 08854-8066
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> radakb.biomaps.rutgers.edu
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Received on Wed Jul 20 2011 - 08:30:03 PDT
