abdul wadood wrote:
Hi, All
I am trying to calculate pmf for enzyme ligand complex using the
tutorial of umbrella sampling.
I have successfully created the unit cell around the protein and have
solvated. The ions were also added by genion.
But when I run the minimization step with the command
grompp -f minim.mdp -c solv_ions.gro -p 3JY0.top -o em.tpr
the following error comes
Fatal error:
Molecule type 'NA+' contains no atoms
I tried my best to solve the problem but could no succeeded.
This is a useless statement. What exactly have you tried? You will receive
help much more efficiently if we know exactly what has worked and what hasn't.
It sounds like a simple problem - you've defined NA+ ions in the topology, but
there aren't any in your system. Be sure that you're not following the tutorial
too literally. That is, just because the tutorial said to add NA+ to that
particular system doesn't mean you'll necessarily have NA+ in every system.
-Justin
Any help to solve this problem will be highly appreciated.
The topology file is attached.
Thanks in advace
Many regards
Abdul Wadood,
Research Scholar,
Dr.Panjwani Center for Molecular Medicine and
Drug Research,
International Center for Chemical and
Biological Science,
University of Karachi, Karachi-75720, Pakistan.
Email:wadoodbiochem...@hotmail.com
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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