Dear Amber users,
I am trying to run a simulation using implicit solvent with ff99sb
force field. When I submit the job, after some time it shows the following
error:
| MPI Timing options:
| profile_mpi = 0
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
and the job stops. I looked for suggestions in the mailing list, where some
people have already faced these problems. I looked at the following link
http://structbio.vanderbilt.edu/archives/amber-archive/2009/1529.php and
found that in my .rst file also, there is a streth of ********* lines. But
as it is an implicit solvent simulation, I can not use ntb=1 and iwrap=1.
My input file is as follows:
zed Born, 12 angstrom cut off
&cntrl
imin = 0, ntb = 0
igb = 5, alpb=1, ntpr = 2500, ntwx = 2500,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 15000000, dt = 0.002,
cut = 12.0
/
Please let me know that could be the solution for this or am I doing any
mistakes in the input file.
Thanking you,
Regards
Aditya.
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Received on Tue Jun 18 2013 - 09:00:02 PDT
