On May 22, 2014, at 3:08 PM, Lara rajam <lara.4884.gmail.com> wrote:
> 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
To add on to Soumendranath's comment, the only time you should _ever_ add counterions is when you are running a system in explicit solvent. If this is your complex topology file for MM/PBSA calculations, salt effects are taken into account with a Debye-Huckel parameter for GB or explicitly in the Poisson-Boltzmann equation. Explicit counterions should not be used here.
I suggest familiarizing yourself with the basic concepts of solvation (both implicit and explicit) if you need more clarity on this topic.
As for the error message you got, see Soumendranath's answer or the beginning of the Amber manual that discusses the use of ions.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 22 2014 - 15:00:03 PDT
