On 8/7/14, 6:44 AM, neha bharti wrote:
Hello All
I am trying to perform MD for protein-ligand complex in popc lipid with
Charmm36 force field and also follow Justin A. Lemkul tutorial.
I performed
perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat
followed by energy minimization then,
perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat
followed by energy minimization then after 16 iteration of scaling down by
0.95 I got Area per lipid: 1.00 nm^2.
In 17th iteration Area per lipid become 0.80 nm^2. but after that when I
visualize the .gro file i.e system_shrink17.gro the ligand molecule is far
from protein and out of lipid.
But till 16th iteration its inside the lipid in its normal position.
Should I perform till 16th iteration which gives area per lipid 1.00 nm^2 ?
Is it a good value for Area per lipid ??
Absolutely not. That's 100 A^2.
InflateGRO doesn't know how to deal with ligands. You need to add the ligand in
after building the protein-membrane system.
-Justin
or there is some error in my files.
My topology file is :
; Include forcefield parameters
#include charmm36_lipid.ff/forcefield.itp
; Include Position restraint file
#ifdef POSRES
#include posre.itp
#endif
This position restraint file does not correspond to any [moleculetype] and will
have no effect when used (more likely you'll get a fatal error). If this is
related to the protein, leave its original location alone.
-Justin
; Include ligand topology
#include LIG.itp
; Ligand position restraints
#ifdef POSRES
#include posre_LIG.itp
#endif
[ moleculetype ]
; Namenrexcl
Protein 3
[ atoms ]
.
.
.
.
.
.
; Strong position restraints for InflateGRO
#ifdef POSRES_STRONG
#include strong_posre.itp
#endif
; Include POPC chain topology
#include popc.itp
; Include water topology
#include charmm36_lipid.ff/tip3p.itp
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcxfcyfcz
11 1000 1000 1000
#endif
; Include topology for ions
#include charmm36_lipid.ff/ions.itp
[ system ]
; Name
Gyas ROwers Mature At Cryogenic Speed
[ molecules ]
; Compound#mols
Protein 1
LIG 1
POPC 128
Please Help
Thank you very much.
With Regards
Neha bharty
--
==
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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