[gmx-users] 100-quartz force field for GROMACS using CGenFF
igladich at sissa.it
Mon Mar 6 07:47:26 CET 2017
thank you for your prompt answer.
I will contact you off-list.
On 2017-03-05 17:14, Justin Lemkul wrote:
> On 3/5/17 6:56 AM, Ivan Gladich wrote:
>> Dear all,
>> I would like to simulate an alpha-quartz (100)
>> interface using GROAMCS.
>> Force field parameters and structure are available in CHARMM
>> (http://mackerell.umaryland.edu/charmm_ff.shtml) and reported in the
>> supplemental material of Lopes, P.E.M., Murashov, V., Tazi, M.,
>> Demchuk, E. and
>> MacKerell, Jr., A.D. "Development of an Empirical Force Field for
>> Application to the Quartz-Water Interface," Journal of Physcial
>> Chemistry B 110:
>> 2782-2792, 2006.
>> Since I am not familiar with CHARMM force field (and crystal
>> simulations as
>> well), my plan was to create the FF in CHARMM and then convert it to
>> format. I copied the quartz (100) structure reported in the paper
>> converting it in .mol2 format, adding PBC information (see mol2
>> attached below).
>> Then I tried using CHARMM General Force Field (CGenFF) program
>> (https://cgenff.paramchem.org) uploading my .mol2 file. If I
>> correctly, the quartz parameters reported in the paper above should be
>> in CGenFF program. However, I am getting error of the type:
>> "Now processing molecule Q100 ... attype warning: element not
> The parameters you need are not part of CGenFF at all. They're CHARMM
> force field parameters and are distinct from CGenFF. They're in the
> "silicates" subdirectory of the CHARMM toppar files available from the
> link you quote above.
>> Since I read from this mailing list that some of you currently use
>> CGenFF, I
>> would like to ask whether some of you have some advise on
>> how to get this force field for this structure running in GROAMCS,
>> using CGenFF
>> or any other alternative way.
> This will require additional force field files (those found in
> "silicates") to be converted to GROMACS format. Contact me off-list
> if you need help doing this; there are various niche parts of the
> CHARMM force field that I haven't converted simply because no one has
> needed them and I don't have test cases for them.
> I don't know anything about such structures, so the subsequent
> application of the parameters is something you'll have to figure out,
> likely by constructing a topology using gmx x2top.
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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