[gmx-users] PMF

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 23 12:47:09 CEST 2010

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.


> 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:wadoodbiochemist at hotmail.com


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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