[AMBER] number of frames read in mmpbsa.py

From: Chris Chris <alpharecept.yahoo.com>
Date: Wed, 23 Mar 2011 09:44:41 -0700 (PDT)

Please help me understand my issue here. I have run two simulations in series,
the first for 5ns and the second for 5 ns. The second 5ns simulation is merely a
continuation of the first. My prod.in file for the production simulation is as

  cut=8.0, ntb=2, ntp=1, taup=2.0,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
thus, I am generatring a frame per ps, correct? If so, the 2 simulations must
comprise 10,000 frames- is this assumption correct?

I am interested in reading frames 6,000-8,000 into mmpbsa.py and thus obtain
binding data. I have the submit file for mmpbsa.py as follows:

mpirun  -np 4 /gpfs1/apps/chemistry/amber/amber11/bin/MMPBSA.py -O -i
mmpbsa_g1tetra.in -o G1TETRA_RESULTS_MMPBSA.dat -sp g1tetra.top -cp
g1tetra_nosolv.top -rp g1tetra_dimer1_no
solv.top -lp g1tetra_dimer2_nosolv.top -y g1tetra_prod_mdx*

My thinking is that the program will read in both trajectories and choose frames
6,000-8,000 and process them. However, this does not work as I get the following
error message:

FYI ptrajSetupIO(): trajin stop value (8000) is greater than the number of sets
read in.
Setting stop to the maximum value (5000)
WARNING in ptrajSetupIO(): trajectory start is > stop; no
configurations will be processed

Thus, only 5,000 frames are read. However- 10,000 should be present.

Can anyone help me with this?


AMBER mailing list
Received on Wed Mar 23 2011 - 10:00:03 PDT
Custom Search