Sorry, I misremembered that. The correct Rmin/2 is 1.7683.
On Wed, Jul 20, 2011 at 12:21 PM, Brian Radak <radak004.umn.edu> wrote:
> Thanks, that's good to know.
>
> I'm a somewhat experienced CHARMM user, so I've encountered the TIP3P
> hydrogen problem before. I don't recall ever hearing a specifically
> convincing argument as to why it is necessary, only that "it shouldn't
> matter too much." There is also the equally befuddling change of the oxygen
> Rmin/2 value from 1.7681 to 1.7682 (the former being listed in the Jorgensen
> paper, the latter in all CHARMM prm files). I suspect I am preaching to the
> choir on this one.
>
> Just for my own edification, is there another paper to be referenced for
> the "alternate" TIP3P model? It seems disingenuous to say one and mean the
> other.
>
> Brian
>
>
> On Wed, Jul 20, 2011 at 12:09 PM, Marc van der Kamp <
> marcvanderkamp.gmail.com> wrote:
>
>> A few comments:
>> - Yes, Amber11 will read/understand the CHAMBER prmtop just fine.
>> - Some bugs can occur during conversion, however (which may not affect the
>> simulations). One thing to check is if your water molecules are all seen
>> as
>> separate molecules - I've seen that the first water molecule is sometimes
>> 'included' in a solute molecule. (which is annoying for selections,
>> imaging
>> or stripping a trajectory from solvent)
>> - Not crucial of course, but you won't be able to use ambpdb with CHAMBER
>> prmtops. (ptraj is fine)
>>
>> NB The CHARMM TIP3P is somewhat different from the original TIP3P,
>> see Jorgensen, et al. (1983) Comparison of simple potential functions for
>> simulating liquid water. J. Chem. Phys. 79, 926-935.
>>
>> --Marc
>>
>> On 20 July 2011 16:52, Brian Radak <radak004.umn.edu> wrote:
>>
>> > 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.
>> > > > _______________________________________________
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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.
>> > _______________________________________________
>> > AMBER mailing list
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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.
>
>
--
================================ 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 - 09:30:03 PDT
