Pancham,
I do not often (never in fact) use GB, but I think your cutoff should be
very large (perhaps 999.0) when using ntb = 0.
You might also try using a larger value for ncyc. I believe it is somewhat
common (at least for me) to see some instabilities after a large number of
conjugate gradient steps. I frequently set ncyc = maxcyc and run only
steepest descent minimization.
Somebody please correct me if I am wrong/under experienced on either
account.
Regards,
Brian
On Wed, Oct 12, 2011 at 9:04 AM, pancham lal gupta <
panchamlalgupta.gmail.com> wrote:
> Hi........
> i was doing energy minimization heme bounded cytochrome P-450,
> with this minimization script
>
> Initial minimization of protein
> &cntrl
> imin=1,
> maxcyc=1000,
> ncyc=100,
> ntb=0,
> igb=1,
> cut=12,
> /
> after ligand replacement i have got many structure with diffrent
> orientations......
> when i have done energy minimization of them some structure is giving NaN
> and some structure is giving energy value after running to all
> step.........
>
> what should i do to get energy value for all the structure ? because
> finally
> i have to compare them
> plz help me...........
>
>
>
> pancham
> IIT DELHI
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Wed Oct 12 2011 - 07:00:04 PDT
