[gmx-users] Running iteration for lipid shrinking using InflateGRO methodology

[Yogesh Sharma]

hello users,

I am using inflategro methodology  to pack lipids around membrane protein.
I used bash script for iteration cycle provided by Justin Lemkul
*. *
But unexpectedly, cycle is dying here
























*gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro
-pbc molWill write gro: Coordinate file in Gromos-87 formatReading file
system_inflated_em.tpr, VERSION 5.1.2 (single precision)Reading file
system_inflated_em.tpr, VERSION 5.1.2 (single precision)Select group for
outputGroup     0 (         System) has  9330 elementsGroup     1 (
 Protein) has  2882 elements.....................Group    12 (
 Other) has  6448 elementsGroup    13 (           POPC) has  6448
elementsSelect a group: Selected 0: 'System'Reading frames from gro file
'POPC', 9330 atoms.Reading frame       0 time    0.000   Precision of
system_inflated_em.gro is 0.001 (nm)Using output precision of 0.001
(nm)Last frame          0 time    0.000
########################################## RUNNING SHRINKING ITERATION
{1..26}...#########################################run_inflategro.sh: 32:
run_inflategro.sh: Illegal number: {1..26}*

I used given ( justin lemkul

minim_inflategro.mdp)

with nstlist modified to 10.
 where is it going wrong.
Previous commands:

gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top
-r system_inflated.gro -o system_inflated_em.tpr

gmx mdrun -deffnm system_inflated_em

gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o
tmp.gro -pbc mol
mv tmp.gro system_inflated_em.gro

perl inflategro.pl system_inflated_em.gro 0.95 DPPC 0
system_shrink1.gro 5 area_shrink1.dat

sh run_inflategro.sh