Dear Amber
I have gone through the amber advanced tutorial
http://ambermd.org/tutorials/advanced/tutorial3/section1.htm
I followed the same to the molecules of my interest ( protein and ligand
complex )
I have a problem in generating the initial prmtop files
I followed the steps
loading the frcmod of ligand
loading protein
combining the protein and ligand
set default PBRadii mbondi2
saved the parmtop and inpcrd for the protein , ligand and complex
The complex need counter ion so i added Na+ to neutralize the charge and
then solvated with the box of 12 A
when i attempt to save the prmtop file it said error
For atom: .R<Na+ 114>.A<Na+ 1> Could not find vdW (or other) parameters for
type: Na+
how can i fix this to generate the prmtop file so that i can use these
files for later mmpbsa calculations
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 22 2014 - 12:30:02 PDT
