[gmx-users] Error while running InflateGRO File

[neha bharti]

Hello All

I am trying to perform MD for protein ligand protein complex in popc lipid
with charmm36 force field and also follow Justin A. Lemkul tutorial.

I generated small molecule topology file from SwissParam which provides
.pdb file for ligand molecule.
I don't have .gro file for small molecule thats why I have created all the
file in .pdb file format.

when I run:

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

it gives error :

Use of uninitialized value $box_x in multiplication (*) at inflategro.pl
line 339.
Use of uninitialized value $box_y in multiplication (*) at inflategro.pl
line 340.
Scaling lipids....
There are 0 lipids...


How to work with .pdb file to run inflategro.pl command??

can anyone please help me out how to solve this error.

Thanks in advance