[gmx-users] ligand binding

[Justin Lemkul]

On 8/6/14, 10:11 PM, Meenakshi Rajput wrote:
> hello
> I have used charmm27 force field to parametrize my protein(human serum

CHARMM27 is a nucleic acid force field.  The force field you're using is 
CHARMM22/CMAP, which is bundled (in Gromacs) in the same files.

> albumin,584a.a) and swiss param to provide parameters to the ligand due to
> which coordinates of ligand is changed and active site of protein is also
> completely changed. Can anybody tell me that ligand coordinates should be
> changed after parametrization? or any energy minimisation problem is there.

That depends on what SwissParam is doing; maybe it does energy minimization as 
part of its process.  You don't want it to do that because it will screw up the 
geometry that you need.  If EM can be disabled, do so.  If not, find a new way 
to generate parameters or otherwise just use the original coordinates, not the 
ones from SwissParam (unless you need H added, in which case you'll have to do 
that yourself, but many programs can do it).

> Am i doing right or not? My energy minimization mdp file is here:-
> cpp        = /lib/cpp
> include        = -I../top
> integrator    = steep
> emtol        = 100
> nsteps        = 200
> nstenergy    = 10
> nstxtcout    = 10
> xtc_grps    = Protein
> energygrps    = Protein
> nstlist        = 5
> ns_type        = grid
> rlist        = 1.4
> coulombtype    = PME
> rcoulomb    = 1.4
> rvdw        = 1.4

These nonbonded settings are incorrect for CHARMM force fields.  You need 
force-switching for van der Waals and the longest cutoffs should be 1.2.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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