AMBER Archive (2007)

Subject: AMBER: Implicit/Explicit solvation

From: Eddie Men (pckboy_at_gmail.com)
Date: Wed Nov 21 2007 - 01:03:12 CST


I am trying to run an implicit/explicit solvation calculation, and my
input is that in the manual.

Sample water CAP simulation with PB reaction field correction
&cntrl
ntx=1, irest=0, imin=0,
ntpr=500, ntwx=500, ntwr=5000,
nstlim=100, dt=0.001,
ntt=1, temp0=10, tempi=10, tautp=0.1,
igb=10, ntb=0, cut=0, fcap=1.0, ivcap=0,
ntc=2, ntf=2, tol=0.000001
/
&pb
npbverb=0, npbgrid=1000, nsnbr=25, nsnba=5,
epsin=1.0, epsout=80.0,
space=0.7, accept=0.001,
smoothopt=1, dbfopt=0,
npopt=0,
cutres=12, cutnb=9, cutfd=9
/

My output however is something like
this:
 PB warning in pb_miccg(): CG maxitn exceeded!

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 NaN NaN 0.0000E+00 N 1

 BOND = 515.0425 ANGLE = 1263.6023 DIHED =
4672.6459
 VDWAALS = ************* EEL = -35804.5153 EPB
= NaN
 1-4 VDW = 2355.3258 1-4 EEL = 24060.2189 RESTRAINT =
0.0000
 ECAVITY = 0.0000 EDISPER = 0.0000

Any idea what is causing this?.

I have a water cap on a region of a protein. Is that possible to model
or did I miss something?.

Thanks for the help

Eddie

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