[gmx-users] Error in inflategro.pl

[Justin Lemkul]

On Mon, Aug 4, 2014 at 5:30 AM, neha bharti <nehabharty123 at gmail.com> wrote:

> 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??
>
>
You can't.  The script needs a .gro file.  If you have a .pdb file, just
use editconf to convert to .gro.

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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