Thank you for the suggestions! I frequently forget about the numerous
conversion programs included in AmberTools.
I was able to produce a parm7 file from a CHARMM psf and this appears to
have the LJ parameters that I want (even the baffling non-zero epsilon terms
on TIP3P hydrogens). However there are, as was indicated, many extra
sections that I am not used to. Am I correct in assuming that AMBER11 will
handle these just fine? I'm a bit use to manually mucking with parm7 files,
but I'm afraid I might break these new and exotic CHARMM sections.
Brian
On Wed, Jul 20, 2011 at 11:16 AM, Marc van der Kamp <
marcvanderkamp.gmail.com> wrote:
> 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
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
> _______________________________________________
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>
--
================================ 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
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Wed Jul 20 2011 - 09:00:03 PDT
