AMBER Archive (2008)

Subject: AMBER: PMEMD and polarized force field ff 02

From: Abhishek Singh (
Date: Thu Jul 03 2008 - 09:53:36 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.
PMEMD input file is
 heat/dynamics holding RNA fixed
   ntxo=1, ntrx=1,
   cut=9.0, tempi=100.0, ntwprt=0,
   ntpr=100, ntwx=500, ntwe=500,
   nstlim=10000, temp0=300.0,
   ntc=2, ntf=2, tol=0.00001,
   tautp=0.2, t=0.0, vlimit=20.0, comp=44.6,
   ntx=1, irest=0, dielc=1.0, ibelly=0,
   ntb=2, ntp=1, pres0=1.0, taup=0.2,
   scee=1.2, dt=0.002,
   ntt=1, ntr=1,ipol=1,
RES 1 32

With Regards,

Abhishek Singh

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