AMBER Archive (2008)

Subject: AMBER: PMEMD and polarized force field ff 02

From: Abhishek Singh (asingh7_at_ncsu.edu)
Date: Thu Jul 03 2008 - 09:50:00 CDT

Dear All
I have a situation that I am simulating rna molecule in a TIP3PBOX using
ff02 force field and salt libraries ionsjc_tip3p. While equilibration there
is a protocol PMEMD that has input file as shown below. Now if i use the
flag ipol=1 in all my sander input files the simulation crashes.
Now two options
1) I tried to skip this stage then got trouble when in last step of
minimization when i have no constrains on the RNA molecule.
2) if i turn off the flag igb=0 then it kills my periodic boundary
conditions of the solvation box.
Kindly suggest how can i run md without PME.

With Regards,

Abhishek Singh

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