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 - 09:00:03 PDT
