[gmx-users] PMF

abdul wadood wadoodbiochemist at hotmail.com
Mon Aug 23 08:23:39 CEST 2010

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.
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 

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