[gmx-users] 100-quartz force field for GROMACS using CGenFF

Ivan Gladich igladich at sissa.it
Mon Mar 6 07:47:26 CET 2017

Dear Justin,

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) 
>> hydroxylated/hydrogenated
>> 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 
>> Silica.
>> 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 
>> GMX
>> format.  I copied the quartz (100) structure reported in the paper 
>> above,
>> 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 
>> understand
>> correctly, the quartz parameters reported in the paper above should be 
>> present
>> in CGenFF program. However, I am getting error of the type:
>> "Now processing molecule Q100 ... attype warning: element not 
>> supported;skipped
>> molecule."
> 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
> --
> ==================================================
> 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
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================

More information about the gromacs.org_gmx-users mailing list