Thank you very much, Dave, for pointing me to the inconsistencies with
respect to the prmtop, coordinate and input files. I realized the mistake
I made. I had initially run SANDER without periodic boundary conditions
and mistakenly using the output coordinates from that run to continue the
minimization with the PMEMD using the prmtop with a periodic box. I have
rectified this issue and now the job is running successfully on one of the
nodes in gyges.
Shashi
On Wed, Jan 23, 2013 at 5:43 PM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jan 23, 2013, Shashidhar Rao wrote:
>
> > I have encountered the following error (the last few lines of the output
> > file have been included below) when running minimization using pmemd.MPI
> on
> > an 8-processor node.
>
> > Error: ifbox=2 in prmtop but angles are not correct
> > Input errors occurred. Terminating execution.
>
> You are using a periodic prmtop (with a bounding box), but trying to to a
> nonperiodic calculation (with ntb=0). This won't work. Admittedly, the
> error
> message is a little obscure. But you need to make a non-periodic prmtop if
> you want to run generalized Born simulations.
>
> I'm not sure why a single-cpu calculation worked. Are you sure you were
> using
> pmemd (not sander) and the identical input and prmtop file?
>
> ...dac
>
>
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--
Shashidhar N. Rao
3 SERINA DRIVE
PLAINSBORO
NEW JERSEY 08536 USA
shashidharr.gmail.com
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Received on Thu Jan 24 2013 - 08:30:02 PST
