Dear Alex,
If you check the manual, under the 'optimize' command you will find all
the default values for each possible parameter. That is how modeller
runs by default. If you do not like the default values , you can change
any of them as you wish.
there are 5 pre set optimization protocols 'refine_1' 'refine_2'
..'refine_5' . The higher the number the more extensive the MD
simulation. As a first approach you could play with these, without
setting every param individually.
Andras
>
> Dear all,
>
> It is possible, that you have received this message already.
> I would like to optimize a protein model using molecular dynamics approach,
>
> but I have a problem with choosing of parameters for OPTIMIZE command
>
> (MD_TIME_STEP, MAX_ITERATIONS, TEMPERATURE etc).
>
> Does anybody know a suitable MD script for model optimization in Modeler 6.2?
>
> Thank you very much for your kind help!
>
> With best regards,
>
> Alex Bazilevsky
>
> ------------------------------
>
> Alex Bazilevsky
> PhD student
> Protein Engineering Departmant
> Institute of Molecular Biology & Genetics
> 150 Acad. Zabolotnogo Street
> Kiev, 03143, Ukraine
> Tel.: 38 044 266-5589, Fax: 38 044 266-0759
>
> E-mail:
>
>
>
>
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras