[gmx-users] Problem in Ligand-Protein complex in POPC
nehabharty123 at gmail.com
Mon Aug 11 09:33:23 CEST 2014
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
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
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
before solvating the system with water.
Is this the right way or I have to do it by another way??
More information about the gromacs.org_gmx-users