Sorry to keep filling inboxes, but I stand corrected yet again.
The original Jorgensen paper does not report Rmin and epsilon values, but
rather A and B coefficients (they use A and C actually). I was taking my
numbers from a secondary source (shame on me). The AMBER and CHARMM values
are in fact different, but this seems to be a matter of rounding preference
more than anything else. It still strikes me as unsatisfying, though I
guess not surprising, that the AMBER and CHARMM communities have adopted
different values for the same model, however computationally equivalent they
may be.
As for the small epsilons on hydrogen, they were a modification to avoid
oxygens and hydrogens from overlapping in a "Coulomb catastrophe." I guess
it would seem that algorithmic improvements would preclude this from
happening in modern software (maybe not in Monte Carlo simulations?)? The
modification does constitute a fundamentally different model in the
literature:
Neria, E., Fischer, S., and Karplus, M. J. Phys. Chem. 1996, 105, 1902.
Maybe this should be mentioned in the AMBER manual?
Thanks to Lennart Nilsson over at the CHARMM forums for enlightening me on
all of this.
Brian
On Wed, Jul 20, 2011 at 12:23 PM, Brian Radak <radak004.umn.edu> wrote:
> 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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>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > > >
>>> > > _______________________________________________
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>>> > > AMBER.ambermd.org
>>> > > http://lists.ambermd.org/mailman/listinfo/amber
>>> > >
>>> >
>>> >
>>> >
>>> > --
>>> > ================================ 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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>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>> >
>>> _______________________________________________
>>> 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.
>
>
--
================================ 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 - 13:30:03 PDT
