Hello Mr. Jason,
Yes I used parmed.py and xparmed.py both.
In both case 'Determining validity of prmtop'
has come. But I have got no other thing even after a long time.
Thanking you.
Sanjib
On Tue, May 20, 2014 at 9:01 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, May 20, 2014 at 11:23 AM, Sanjib Paul <sanjib88paul.gmail.com
> >wrote:
>
> > hii,
> > I am working on a metalloprotein HCAII, which contains zinc. In one
> > configuration zinc is bonded with three nytrogen atoms and a oxygen atom
> of
> > water molecule and in another it is bonded with three nytrogen atoms and
> a
> > oxygen atom of hydroxide ion. I am doing simulation by following steps.
> 1)
> > minimization, 2) heating, 3) NVT equilibration . 4) NPT equilibration 5)
> > NVT production. In first case I am getting error during NPT equilibration
> > but in second system I got in heating step. (minimization has been done
> by
> > pmemd.cuda only). In both case I got same error message but in first case
> > one message extra which is coming during NPT equilibration.
> >
> > * ERROR: PMEMD does not support intermolecular PRFs*!
> >
> > I wrote other error message in my earlier mail. So, is the error coming
> due
> > to my systems which contain four metal-nonmetal bond? Or, is there any
> > other reason? I am trying to trying to compile MPI version of pmemd.cuda
> by
> > other MPI rather than OpenMPI.
> >
>
> ​Did you use "checkValidity" in ParmEd like I suggested?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue May 20 2014 - 10:00:03 PDT
