Hello,
On Wed, Mar 31, 2010 at 11:02 AM, imtiaz shafiq <imtiazshafiq.gmail.com> wrote:
> I having some trouble in pKa Calculations Using Thermodynamic Integration.
>
> As a test run I have downloaded asph_model.prmtop, asph_model.incprd,
> asp_model.prmtop and asp_model.inpcrd from amber tutorials page.
>
> I have also downloaded
>
> model_step2.mdin
>
> model ASH to ASP for pKa calculation
> &cntrl
> nstlim =3000000, nscm=2000,
> ntx=5, irest=1, ntpr=1000,
> tempi=300.0, temp0=300.0, ntt=3, gamma_ln=5.0,
> ntb=0, igb=5, cut=999.0,
> dt=0.001,
> ntc=2, ntf=2,
> ntwr = 10000, ntwx=1000, ntave=1000
> icfe=1, clambda=0.11270,
> /
>
>
> and
>
> -O -i model_step2.mdin -p asph_model.prmtop -c asph_model_step1.rst -o
> asph_model_step2.out -inf asph.mdinfo -x asph_model_step2.mdcrd -r
> asph_model_step2.rst
> -O -i model_step2.mdin -p asp_model.prmtop -c asp_model_step1.rst -o
> asp_model_step2.out -inf asp.mdinfo -x asp_model_step2.mdcrd -r
> asp_model_step2.rst
>
> model_step2.group
>
> Now when I am runing the job
>
> mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2 -groupfile model_step2.group
>
> I am getting the following error
>
>
> [imtiaz.cluster1 ti-tut6]$ mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng
> 2 -groupfile model_step2.group
>
> Running multisander version of sander amber10
>
> Total processors = 2
> Number of groups = 2
>
>
> Unit 30 Error on OPEN: asph_model_step1.rst
These are examples. This groupfile corresponds to the second step in
TI where the restart file of the first step is used as the coordinate
file for the second. Since you never ran the first step, the restart
file for that step was never created, so it can't be found here (hence
the explanatory error: Error on OPEN: asph_model_step1.rst).
If you read the tutorial it details these points. The files provided
are not enough to run this simulation blindly, you need to follow the
instructions and set up your own files (using the provided ones as
templates).
Good luck!
Jason
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code. This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 9100 failed on node n1 (10.0.0.1) with exit status 1.
> -----------------------------------------------------------------------------
>
> What could be the possible reason? How I can fix this issue?
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 31 2010 - 08:30:05 PDT
