[gmx-users] Error in grompp for protein-ligand tutorial

[Justin Lemkul]

On 1/27/14, 2:15 PM, José Adriano da Silva wrote:
>   I am new to Gromacs, then follow the tutorial protein-ligand, decided to
> adapt the procedure for my protein (acetylcholinesterase) and my binder. The
> procedure is this (protein-ligand complex):
>
>
>
>
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp
> lex/index.html>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl
> ex/index.html
>
>
>
> Well, I switched to facilitate the name of my protein and my binder by the
> names used in the tutorial. The problem occurs when I do the command:
>
>
>
> grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
>
>
>
>
> The following error occurs:
>
>
>
> Fatal error:
>
> Molecule type 'Protein_chain_A' contains no atoms
>

The error suggests that the topology is probably empty, which you can inspect 
with a text editor.  Maybe pdb2gmx failed, but the fatal error from that step 
should have been quite obvious.  Otherwise, some modification that you have made 
to the topology has rendered its format unintelligible.

-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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