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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jul 31 2014 - 21:00:02 PDT
