[gmx-users] issue regarding gromacs software

Justin Lemkul jalemkul at vt.edu
Sat Feb 16 00:01:08 CET 2019

On 2/15/19 12:17 PM, suchita sakore wrote:
> Respected sir/madam,
> I am doing a project under my post graduation.  I am doing a simulation of
> a lipid ion channel by using gromacs software. I am facing problem while
> generating the gro file. I have built peptide by using discovery studio
> software.
> while running the following command :
> gmx_mpi pdb2gmx -f pep.pdb -o pep.gro
>   The error seen is that the molecule is undefined in the PDB format. The
> gromacs software is  not able to recognize the molecule. I am attaching
> here the file on which I am working right now. Kindly resolve my problem as
> soon as possible. I am waiting for your answer.

The mailing list does not accept attachments.

Please always report errors exactly from the terminal, copied and 
pasted. We can't help if we don't know what the actual error was.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


More information about the gromacs.org_gmx-users mailing list