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

[neha bharti]

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??

Please Help.


With Regards
Neha Bharty