[gmx-users] Problem in Ligand-Protein complex in POPC

Justin Lemkul jalemkul at vt.edu
Mon Aug 11 13:35:15 CEST 2014

On 8/11/14, 3:33 AM, neha bharti wrote:
> Hello All
> I am trying to perform MD for protein-ligand complex in POPC with charmm36
> force field and also follow Justin A. Lemkul tutorial using Gromacs VERSION
> 4.5.5.
> As I am working on Protein-Ligand complex I am having few queries:
> 1) The .pdb file was oriented along the z-axis using editconf -princ,
> followed by a rotation. We have to perform this step before separating the
> protein and ligand from the pdb file so that ligand also rotated along the
> same axis??
> 2) For orientation I use the following command.
> editconf -princ -f protein.pdb -o protein_princ.pdb
> editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb
> But when I include the POPC then saw that  The protein is parallel align
> with popc which is not correct.
> I also use
>   editconf -rotate 0 90 0 -f protein_princ.pdb -o protein_princ_rotate.pdb
> but still the alignment is same.
> Should I use only editconf -princ command and skip the rotation part or
> what else I can do??
> 3) As* InflateGRO* script can not deal with ligand. So when should I
> include my ligand file in protein??
> I have included it before system creation and at the time of using
> *InflateGRO* script I remove my ligand file and again insert it after
> perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5
> area_shrink1.dat
> before solvating the system with water.
> Is this the right way or I have to do it by another way??

You can tell for yourself if it's right if the ligand is positioned correctly 
after preparing the rest of the system.  If the protein was suitably restrained, 
it should be.



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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