[gmx-users] change in rename of 1POPC to 1LIG though coordinate and atom same in 1LIG of 1POPC, during solvation of system

Sangita Kachhap sangita at imtech.res.in
Wed Jun 6 09:09:03 CEST 2012

Hello all
I have to do MD simulation of membrane protein having docked ligand in POPC
lipid bilayer.
I am geeting error during solvation of system:
Resname of 1POPC in system_shrink1.gro converted into 1LIG

I have done following:


1) Generate topol.top using GROMOS96 53A6 parameter set
pdb2gmx -f 3gd8-mod.pdb -o 3gd8-mod-processed.gro -water spc

at prompt select 14

2) Download:
    * popc128.pdb - the structure of a 128-lipid POPC bilayer
    * popc.itp - the moleculetype definition for POPC
    * lipid.itp - Berger lipid parameters

from http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies

3) Modify topol.top with:
#include "gromos53a6.ff/forcefield.itp"


#include "gromos53a6_lipid.ff/forcefield.itp"


; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
; Include ligand topology
#include "ligand-full.itp"

; Include POPC chain topology
#include "popc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

and at the end add LIG  1 in [molecules]

4) cp files

from gromacs top to directory named gromos53a6_lipid.ff in working directory.
Append parameter ([ atomtypes ], [ nonbond_params ], and [ pairtypes ])from
lipid.itp to ffnonbonded.itp & ffbonded.itp and create a forcefield.doc file
that contains a description of the force field parameters contain "GROMOS96 53A6
force field, extended to include Berger lipid parameters".
Delete line ";; parameters for lipid-GROMOS interactions." and its subsequent
line, change HW as H of [ nonbond_params ]

5) Generate .tpr for POPC
grompp -f minim.mdp -c popc128a.pdb -p topol_popc.top -o em.tpr -maxwarn 1
(change OW1, HW2, HW3 to OW, HW and HW2 respectively)

6) Remove periodicity
trjconv -s em.tpr -f popc128a.pdb -o popc128a_whole.gro -pbc mol -ur compact
(at command prompt select 0)

7) Oriant the protein within the same coordinate as written in end of
editconf -f 3gd8-mod-processed.gro -o 3gd8-mod-processe_newbox.gro -c -box
6.23910 6.17970 6.91950

8) Pack lipid around protein
cat 3gd8-mod-processe_newbox.gro popc128a_whole.gro > system.gro

Remove unnecessary lines (the box vectors from the KALP structure, the header
information from the DPPC structure and update the second line of the
coordinate file (total number of atoms) accordingly.

9) Modify topol.top to add positional restrain on protein

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"

; Strong position restraints for InflateGRO
#include "strong_posre.itp"

; Include DPPC chain topology
#include "dppc.itp"

; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"

Genrate new positional restraint
genrestr -f 3gd8-mod-processe_newbox.gro -o strong_posre.itp -fc 100000 100000
for system (protein + ligand)
Add a line "define = -DSTRONG_POSRES" to .mdp file

10) addion POPC 128 to topol.top

11) Scale down lipid
perl inflategro.pl system.gro 0.95 POPC 0 system_shrink1.gro 5 area_shrink1.dat

12) Solvate with water

Copy vdwradii.dat from Gromacs top to working directory and change the value of
C from 0.15 to 0.375(to avoid addition of water in lipid hydrohphobic core)

genbox -cp system_shrink1.gro -cs spc216.gro -o system_shrink1_solv.gro -p

Upto 11th step .gro file is OK conatin protein resid 32-254, ligand 1LIG, POPC
resid 1-128 and solvent

After 12th step in gro file protein is there 32-254, Ligand 1LIG but POPC resid
2-128 because resid 1 of POPC is converted to 1LIG though all cordinate and atom
name are same of 1POPC in 1LIG.

Anybody please suggest me why this change in rename is occuring.

With regards

सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202

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