Hi Jason,
So Should I strip the IL residues from the mdcrd also?
I already removed the ILs to get my complex.prmtop using the strip_mask (-s)
Vivek
On Thu, Jul 31, 2014 at 9:33 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Thu, Jul 31, 2014 at 11:07 PM, Vivek Shankar Bharadwaj <
> vbharadw.mymail.mines.edu> wrote:
>
> > Hi Jason,
> >
> > Some more Info.
> >
> > The number of atoms in the (complex) = number of atoms in (receptor +
> > ligand) topology files.
> > However, I am running a simulation of an enzyme in an ionic liquid water
> > mixture. I did consider the IL to be part of the solvent and stripped it
> > when getting the complex prmtop.
> >
> > Could this have anything to do with the NATOM mismatch?
> >
>
> Probably. You probably have to change the "strip_mask" variable to strip
> the IL residues out of your system if you didn't include them in your
> topology file.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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--
Vivek S. Bharadwaj
Graduate Student
Department of Chemical and Biological Engg.
Colorado School of Mines
Golden Colorado
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Received on Thu Jul 31 2014 - 21:00:02 PDT
