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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==
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