[gmx-users] MM dihedral scanning

Justin Lemkul 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
> dihedral.
> 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*)
> http://www.chemspider.com/Chemical-Structure.217102.html?rid=378be046-1c14-4bce-ac46-6591776f7e08
> dihedrals of O-C-CH2-CH3
> http://www.chemspider.com/Chemical-Structure.55178.html?rid=16e49844-d25d-48c8-b1b5-89fb2f9372bd
> dihedral of CH3-N-CH2-CH2
> Many thanks in advance for any suggestion.
> Cheers
> Mohsen


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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