[gmx-users] MM dihedral scanning
jalemkul at vt.edu
Fri Jan 13 00:24:33 CET 2017
On 1/12/17 3:18 PM, Mohsen Ramezanpour wrote:
> Dear Gromacs users,
> For parameterization of a molecule in Charmm36, I have got the QM scanning
> and partial charges from GAMMP server. However, the fitted parameters are
> not good enough.
That's very surprising. What's wrong with what GAAMP gave you?
> I decided to do the MM scanning and try to get better parameters for the
> Unfortunately, I do not have any experience with this part, and I could not
> find any tutorial for how to do this in Gromacs.
> I was wondering if you are aware of any tutorial which could help me to
> overcome this challenging step.
Tutorial (CGenFF theory is the same as CHARMM, by design):
Fitting program and other resources:
Obviously, these are all CHARMM-centric approaches and frankly the modules
within CHARMM make parametrization rather straightforward (not "easy," mind you,
but straightforward). Since I began working with CHARMM, it has become
indispensable in my daily routine.
If you want to do things in GROMACS, the main issue is that you will have to do
MM scans in a more manual fashion, by restraining the target dihedrals (very
strongly) in a series of configurations (typically at intervals of 15 degrees
over a full rotation) while allowing the rest of the molecule to relax to match
the QM. Deactivate the restraint, obtain the potential energy of the molecule
via mdrun -rerun and plot as a function of the dihedral. A bit of shell
scripting and careful topology modification and this can be done.
> There are three parts of molecule which I am interested in its dihedral
> parameters that I am stuck in it for a while:
> 1) (*2,2-Diethyl-1,3-dioxolane*)
> dihedrals of O-C-CH2-CH3
> 2) (DIMETHYLPROPYLAMINE)
> dihedral of CH3-N-CH2-CH2
> Many thanks in advance for any suggestion.
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
More information about the gromacs.org_gmx-users