[gmx-users] DPPC replication error

Priya Das priyadas001 at gmail.com
Tue Nov 25 06:31:20 CET 2014

Dear Sir,

I took 128 dppc.pdb, dppc.itp and lipid.itp from Tielemans site (
http://people.ucalgary.ca/~tieleman/download.html). For my work i need to
replicate 128 dppc.pdb four times to get 512 lipid molecules.

The sequence of commands are as follows:

# replicate 4 boxes of 128 dppc with SOL
$ genconf -f dppc128.gro -o dppcnew.gro -box 2 2 1

# generated .tpr file for new dppc with 512 lipid
$ grompp -f minim.mdp -c dppcnew.gro -p topol_dppc.top -o em.tpr

#removed periodicity
$ trjconv -s em.tpr -f dppcnew.gro -o dppcnew_whole.gro -pbc mol -ur compact

# inserted my protein in new lipid bilayer
$editconf -f 1AKL.gro -o 1AKL_new.gro -c -box 12.41840 12.44350 6.59650

#concatenate protein and lipid
cat 1AKL.gro dppcnew_whole.gro > system.gro


$ perl inflategro.pl system.gro 4 DPPC 0 system_inflated.gro 5 area.dat

*After running inflate.pl <http://inflate.pl>, the protein is centered
in the empty box ; with only  128 lipid. *

*Let us all join hands to save our " Mother Earth"*
Priya Das
Research Scholar
Dept. of Computational Biology and Bioinformatics,
University of Kerala

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