Hi
I am using AMBER8 on a Linux system. I have been trying to resolve a poor
initial model (with clashes) by steepest descent energy minimisation. I
use the input below.
&cntrl
imin=1, nmropt=0,
ntx=1, irest=0,
ntpr=1,
ntf=1, ntb=0,
igb=2, gbsa=1,
ibelly=0,
maxcyc=1000, ntmin=2,
ntc=1, tol=0.0005, jfastw=0,
ivcap=0, fcap=0.5,
cut=99.0,
&end
In the output file:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 6.2047E+12 HG13 160
BOND = 859.0824 ANGLE = 840.4581 DIHED = 302.9558
VDWAALS = ************* EEL = -1870.7016 EGB = -259.3464
1-4 VDW = 8778.4861 1-4 EEL = 1433.5810 RESTRAINT = 0.0000
ESURF = NaN
NSTEP ENERGY RMS GMAX NAME NUMBER
2 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = 52129.9369 DIHED = 189.3636
VDWAALS = NaN EEL = NaN EGB = NaN
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
ESURF = 0.0000
I've tried weighting the energy terms (ALL, RSTAR, INTERN, IMPROP) using
'&wt' to get low values for the energy but minimisation still fails. I'm
wondering if there is anything else I should try? Or must I start with a
good initial model?
Thankyou for your help.
Conan
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Received on Wed Sep 20 2006 - 06:07:19 PDT
