AMBER Archive (2006)

Subject: AMBER: resolving a bad initial model

From: wang_at_cbs.cnrs.fr
Date: Tue Sep 19 2006 - 09:42:11 CDT

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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