Hello,
Does anyone have any experience of modelling small (2-6 residue)
peptides using random conformational analysis procedures? I have
modelled several tripeptides using the Sybyl package and their Random
Search procedure (1000-5000 search iterations) with a distance-based
dielectric constant of 80 to simulate water. I have now submitted a
dipeptide to a similar conformational search except that I have included
explicit waters (using the SILVERWARE algorithm and default settings)
and a constant dielectric function of 80 to simulate bulk water outside
of this solvation box. Specifically, I am interested in knowing two
things:
1. How much longer will this sort of search take (it's been running
nearly a week now!)?
2. Are the conformers found likely to be very different from those that
would have been found using the simpler approximation to water of a
distance-based dielectric function? Since I am interested in modelling
a number of tri- to hexapeptides, the trade-off between computational
time and "reliabilty/accuracy" of results is paramount.
Thanks very much for any help,
Neil
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Neil J. Marshall
Memorial Building Tel: +44 (01248) 351151 Ext. 2367
School of Biological Sciences Fax: +44 (01248) 370731
University of Wales, Bangor E-mail: bss219 at bangor.ac.uk
Gwynedd, LL57 2UW
United Kingdom
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