Re: BALLView - a molecular viewer and modeling tool
Francesco Pietra schrieb:
First, I must congratulate with you and your staff for
this beautiful work. Then, I would like to see in the
future a BAKMDL-type global conformational search in
molecular mechanics. The basic step in any
computational work with natural products, be that
semiempirical or quantum mechanical, is to get a
reliable list of low-lying conformers.
As far as I know we dont have yet features compareable
to BAKMDL, but since we have a confomer library for
the different amino acids, you might write such an
Current work is underway to add further conformer features,
but this will still take some time...
Second, I have not yet examined in full the
possibilities of your MD. I have seen on internet that
there is a python script for simulated annealing. I'll
try that (and I'll try also to learn python, which I
also need for nwchem). What I expect is that this
simulated annealing procedure offers the possibility
to sample conformers. The beautiful graphics of
ballview could aid grouping similar conformers
together and than subject them to BAKMDL exploration,
once this is implemented.
The beautifull thing about BALLView is, that you can
make use of the full set of BALL features.
Therefore you can easily modfiy the existing annealing
script to use different force fields, settings or
record a set of conformers.
Also have a look at the IDE features, that will ease
your Python scripting:
The video at the bottom.
I have not yet checked if there is a debian amd64
package. The molecules I am interested in (no
polymers, though huge number of degrees of freedom,
require the power of a 64bit multiprocessor machine).
To this regard, is any plan to parallelize ballview
The debian source package available on debian-mentors
allows you to build a binary package from the source
package, including the changes for 64 bit arch.
Unfortunately I cant create a native 64 bit binary package,
since I dont have a corresponding machine.
If you have future questions, independent from the
debian package, feel free to mail me or post on the BALL