[AMBER] pKa Calculations Using Thermodynamic Integration

From: imtiaz shafiq <imtiazshafiq.gmail.com>
Date: Wed, 31 Mar 2010 16:02:49 +0100

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 ASH to ASP for pKa calculation
   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,
   ntc=2, ntf=2,
   ntwr = 10000, ntwx=1000, ntave=1000
   icfe=1, clambda=0.11270,


-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
-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


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
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 ( with exit status 1.

What could be the possible reason? How I can fix this issue?

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Received on Wed Mar 31 2010 - 08:30:02 PDT
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