[gmx-users] can we use Area per lipid: 1.00 nm^2

[Justin Lemkul]

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 ]
> ; Name            nrexcl
> 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       fcx        fcy        fcz
>     1    1       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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================