AMBER Archive (2006)

Subject: Re: AMBER: resolving a bad initial model

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Sep 19 2006 - 09:53:47 CDT

you might want to go into some program that lets you
modify structure by hand. your HG13 (atom 160) has
a gradient of 10^12- that is really huge. it must be right on top
of another atom, so if you can move it manually the forces
might be more reasonable.

wang_at_cbs.cnrs.fr wrote:

>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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