On Thu, Apr 24, 2003, Nick Polfer wrote:
>
> I am using a script file to do an annealing procedure for polypeptides in
> the gas phase. I build these peptides using Xleap (saveamberparm...) and
> generate the initial.crd and prm.top files to do the annealing procedure.
> The initial coordinates of the molecule do not seem to be too close in
> space. The script first minmises the seed structure and then goes through
> annealing cycles; i.e. increasing T to 800 K and controlled cooling to 0 K
> to generate seed structure for next cycle. So far I have never had problems
> using this procedure, however, for this peptide the simulation seems to blow
> up every time.
>
>
> Coordinate resetting (SHAKE) cannot be accomplished, deviation is too large
> NITER, NIT, LL, I and J are : 0 3 63 145 146
You might look at atoms 145 and 146 to see if there is anything funny or
different about them, compared to other peptides where things have worked.
You might also just be on the edge of an instability: we generally do
simulated annealing to those kinds of temperatures with SHAKE turned off, and
that could certainly be an option you might want to consider as well.
...good luck...dac
--
==================================================================
David A. Case | e-mail: case.scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Fri Apr 25 2003 - 00:53:01 PDT
