[gmx-users] (Newbie) Residue SiO2 for solvation?

[Justin Lemkul]

On 6/10/17 7:03 PM, Jose Borreguero wrote:
> Dear Gromacs users,
> 
> I want to encase this mildly hydrated protein
> <http://nbviewer.jupyter.org/github/jmborr/confinedBSA/blob/master/simulation/monomer/solvatedBSA/minimize/relax/stripped_system_h0.17.gif>
> within an amorphous silica cube, so I thought of using gmx solvate. Thus, I
> need a residue for the SiO2 molecule. The OPLS force field includes
> non-bonded parameters for SI atom, but no SiO2 "residue".
> 
> Has anyone gone through this particular problem? Or can anyone give me some
> pointer as to how create a custom residue starting from, say, a PDB file of
> the molecule, and then the steps to "merge" this residue with the rest of
> the OPLS force-field?
> 

The coordinates don't tell you anything about the topology.  OPLS-AA 
parametrization would require an initial QM optimization and calculation of a 
charge distribution, followed by whatever evaluation of condensed-phase 
properties that you can find for that molecule.  Parametrization is inherently 
an advanced topic.

-Justin

-- 
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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

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