[gmx-users] PRODRG -cgnr

Justin Lemkul jalemkul at vt.edu
Sun Jul 27 18:25:54 CEST 2014

On 7/27/14, 11:49 AM, Atila Petrosian wrote:
> Dear gromacs users
> I wan to use PRODRG server to do md simulation of my system (drug-protein
> complex).
> I know charge and cgnr parameters obtained from PRODRG (for ligand
> molecule) are not accurate.
> I know there are 2 ways to solve this problem:
> 1) If there are special functional groups in my ligand, I can find theses
> functional groups being in protein, DNA and RNA molecules. Then I can
> reassign charges and charge groups from these moieties.
> 2) Another way is to get partial charges from QM calculation.
> I have some questions about second way:
> Since the topology (itp file) parameters obtained from PRODRG are based on
> GROMOS force field, I should consider cgnr correctly.
> For example, in ffG43A1, N and H atoms form one charge group (cgnr = 0),
> thus, summation of these charges are zero (-0.280 + 0.280 = 0).
> N     N   -0.280     0
> H     H    0.280     0
> Using QM calulations, I can only obtain partial charges (mulliken charges).
> My main question is that if I obtain partial charges using QM calulations,
> how to set cgnrs?

The first thing to know is that Gromos96 charges bear little resemblance to 
charges you will get from any QM method.  The developers used some DFT 
calculations as a guideline for setting charges empirically; QM has only ever 
been a guide in Gromos96 parametrization.  Long story short, direct application 
of QM charges isn't suitable for this force field.

The other thing to consider is that charge groups are only relevant when using 
the group cutoff scheme in Gromacs; if using Verlet, charge groups are not used. 
  If using the group method, charge groups are assigned such that they contain 
net-neutral or net-integer (+1/-1) charged groups.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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