AMBER Archive (2006)

Subject: Re: AMBER: resolving a bad initial model

From: Andy Purkiss-Trew (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Tue Sep 19 2006 - 09:51:01 CDT

Hi Conan,

Did you do a check when you built the system in leap? This would tell
you if you have superimposed atoms.

And did you follow the instructions for the igb=2 (see the GB part of
the sander section of the manual):

'With this option, you should use the LEaP command "set default PBradii
mbondi2" or "set default PBradii mbondi" to prepare the prmtop file.

If everything was fine here, then as you have 'ESURF = NaN' in the first
step, I'd suggest turning off the surface area part of the forcefield
for the first minimization run. Try gbsa = 0 and/or igb = 6 (which turns
off the complete solvent model). Just run for a 100 steps or something
and then try with your input again.

Andy

On Tue, 2006-09-19 at 16:42 +0200, 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
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu 

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+---------------------------------------------------------------------+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|           E-mail   a.purkiss_at_mail.cryst.bbk.ac.uk                   |
|      Phone 020 7631 6869 (Work) or 0776 490 360 (Mobile)            |
+---------------------------------------------------------------------+

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu