[gmx-users] Error in inflategro.pl
nehabharty123 at gmail.com
Mon Aug 4 13:37:28 CEST 2014
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
Use of uninitialized value $box_y in multiplication (*) at inflategro.pl
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
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