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

neha bharti nehabharty123 at gmail.com
Tue Aug 12 12:50:16 CEST 2014

Thank you very much justin for your reply.

But I am still facing the problem to include ligand in protein.

Following step I am performing:

 PDB file of  protein complex with ligand is taken from pdb

1) editconf -princ -f protein.pdb -o protein_princ.pdb

2) editconf -rotate 0 0 90 -f protein_princ.pdb -o protein_princ_rotate.pdb

3) separate protein and ligand files from protein_princ_rotate and then save
then in different files

protein file: protein_princ_rotate.pdb

ligand file: lig_princ_rotate.pdb

4) generating pdb and itp file for small molecule

5) Generation of topology files for protein:

pdb2gmx -f protein_princ_rotate.pdb -water tip3p -ignh -o protein.pdb

6) mearge protein.pdb and lig.pdb file in conf.pdb file

7) copy the files (mention in tutorial) from charmm36 force field and place
them in new created folder charmm36_lipid.ff

8) Next, create a forcefield.doc file that contains a description of the
force field parameters in it. Mine contains something like:

CHARMM36 all-atom lipid force field (with CMAP), extended to include Berger
lipid parameters

9) changes in topology file "charmm36/tip3p.itp" to

10) Add Ligand Topology file:

; Include ligand topology
#include "lig.itp"

; Include water topology
#include "charmm36.ff/spc.itp"

11) The next adjustment to be made is in the [ molecules ] directive. To
account for the fact that there is a new molecule in conf.gro, we have to
add it here, like so:

[ molecules ]
; Compound        #mols
Protein_chain_A     1
LIG                 1

download the following files:

popc128a.pdb - the structure of a 128-lipid POPC bilayer
popc.itp - the moleculetype definition POPC
lipid.itp - Berger lipid parameters

12) Orient the protein and membrane

Convert the popc128.pdb to .gro format with editconf and remove the initial

(a) Generate a .tpr file for a popc-only system using grompp.

grompp -f em.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr

(b) Use trjconv to remove periodicity:

trjconv -s em.tpr -f popc128a.pdb -o popc_whole.gro -pbc mol -ur compact

select 0 for system

13) orient the peptide within this same coordinate frame as lipid, and place
the center of mass of the peptide at the center of this box:

editconf -f conf.gro -o conf_newbox.gro -c -box 6.23910 6.17970 6.91950

14) Pack the lipids around the protein and ligand complex

First, concatenate the protein and bilayer structure files:

cat conf_newbox.gro popc_whole.gro > system.gro

15) Remove unnecessary lines

16) Now, generate this new position restraint file using genrestr and
include it in topology file:

genrestr -f conf_newbox.gro -o strong_posre.itp -fc 100000 100000 100000

select 0 for system

17)In the .mdp file used for the minimizations, add a line "define =
-DSTRONG_POSRES" to make use of these new position restraints.

18) seperate the ligand and protein file because InflateGRO not deal with
small molecule.

then InflateGRO script run:

perl inflategro.pl system.gro 4 POPC 0 system_inflated.pdb 5 area.dat

19) energy minimize:

grompp -f em.mdp -c system_inflated.gro -p topol.top -o em.tpr

mdrun -v -deffnm em

another script command:

perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat

Another energy minimization step:

grompp -f em.mdp -c system_shrink1.gro -p topol.top -o em.tpr

mdrun -v -deffnm em
Repeat this step.

area per lipid reached  ~69 Å square. Then I stop.

then again include the small molecule to final system_shrink.gro file and
after that I perform the steps that is given in tutorial.

is this the right way. I am doing this because we have to show the
interaction of ligand and protein. I first created the ligand protein
complex and at the time of running inflategro.pl command I separate the
ligand molecule and again include it after iterations of scaling down by

rest of the steps is same as given in tutorial.

one more query can we use orientation of protein in membrane database
for orientation of protein instead of editconf???
as it is not giving me the correct alignment.

please help.

>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
> >force field and also follow Justin A. Lemkul tutorial using Gromacs
> >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
> >protein and ligand from the pdb file so that ligand also rotated along
> >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
> >
> >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
>after preparing the rest of the system.  If the protein was suitably
>it should be.


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