Got worried myself about that recently, Charles said:
"Do note that torsionDB can have large energies - the minima
are not at zero."
? so no worries from energy standpoint. Just make sure there are no serious
outliers, as usual.
On Aug 12, 2014, at 6:25 PM, Sandra Pineda Sanabria <pinedasa at ualberta.ca>
wrote:
> Hi,
>
> I am using anneal_nordc.py and refine_nordc.py for the structure of a
> heterodimer. I noticed that most of the positive energy on my calculations is
> coming from the torsionDB term (~4000, 95% of total Energy) and that 90% of
> torsion angle violations come from residues in the same monomer even if I do
> not use any type of angle restraints, (e.g. dihedrals) for that monomer.
>
> The setup is quite conventional:
>
> from torsionDBPotTools import create_TorsionDBPot
> torsionDB = create_TorsionDBPot('torsionDB')
> potList.append( torsionDB )
> rampedParams.append( MultRamp(.002,2,"torsionDB.setScale(VALUE)") )
>
> But still get:
>
> Powell::step: irregular exit: Line search abandoned: gradient may be
> incorrect
> *-- POWELL ------ step= 4 --- stepsize= 0.01000 --- energy evals=
> 37 -*
> | E(poten)= 4571.8073491 grad= 1.3909215 ANGL=
> 119.5602423 |
> | BOND= 18.4561174 CDIH= 4.8851933 HBDB=
> -182.0507300 |
> | IMPR= 16.1391822 VDW= 73.8122596 Vgyr=
> 4.4490164 |
> | jcoup= 0.0000000 noe= 190.1627641 tDB=
> 4326.3933038 |
>
> *------------------------------------------------------------------------------*
>
> Am I missing something? Should I include a selection argument excluding
> tails? Not append?
>
> Thank you for your help.
> Sandra E. Pineda S.
>
> 419 Medical Sciences Building
> Department of Biochemistry
> University of Alberta
> T6G 2H7 Edmonton, AB, Canada
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