Hi Jason,
I am facing some difficulty to run amber12 where the .prmtop and .inpcrd
files were generated using chamber. Strangely, I don't see any box
information in the inpcrd file and the errors are related with that. Do I
need that information for running sander.MPI. If so, how do I include that.
I tried to add that manually but it doesn't work. These are the control
parameters during that time
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntt = 3,
temp0 = 300.0,
gamma_ln = 2.0,
ntp = 1,
taup = 2.0,
ntb = 2,
ntc = 2,
ntf = 2,
nstlim = 1000,
ntwe = 100, ntwx = 100, ntpr = 200,
/
The error in log file looks like
| Flags: MPI
getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read
| peek_ewald_inpcrd: Box info not found in inpcrd
Another thing, the sander.MPI works for for minimization. the cntrl
parameters are given below for minimization
&cntrl
imin = 1,
maxcyc = 500,
ncyc = 250,
ntb = 0,
igb = 0,
cut = 12
/
Finally, my main aim is to use MMPBSA.py.MPI for the chamber generated
.prmtop file and namd generated .dcd file. I converted the .dcd file to
.mdcrd file and use that file for that calculation but it doesn't work at
all.
Please help me out in this regard. How do I solve this issue.
Best
Sudipta
On Mon, Sep 16, 2013 at 1:24 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, Sep 16, 2013 at 1:05 PM, sudipta <sudipta.mml.gmail.com> wrote:
>
> > Another thing, the chamber generated .prmtop and .inpcrd files can't
> > produce output with amber 9 sander.MPI. However, it is showing sander.MPI
> > is running. That means chamber generated files cannot be used with amber
> 9.
> > Is it true? Although, it is silly but I want to make sure that.
> >
>
> Correct. chamber was developed after Amber 9. If all you have is Amber 9,
> you must use the Amber force field (together with NAMD if you wish) in
> order to use MMPBSA.py.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sun Sep 22 2013 - 08:00:02 PDT
