Hello Simon--
>
> I am attempting to perform some SA on a complex of two proteins, one has
> an elongated shape and the other is roughly spherical. If I do not
> include a collapse term, the two proteins end up inside each other and
> all restraints are thus violated and the VdW energy is huge. If I
> include a collapse term for the entire complex, the proteins remain far
> apart, as they are randomly placed at the beginning of the run. I have
> also try to separate the complex into three separate roughly spherical
> domains, to then calculate the Rgyr for each domain and then to include
> these in three separate collapse assign statements in old xplor
> language, when I do this the collapse term becomes NaN as does the
> gradient and the Epot and Ekin terms. How can I handle this sort of
> complex and get the proteins to move close together without getting too
> close. Do I need an Rgyr term, if so, what form should it take? In the
> SA run bonds, angles, impropers, VdW and PRE terms are all included in
> the XplorPot.
>
This is not behavior which we usually see. Which protocol are you
using as a starting point? This script is probabably a good starting
point:
/home/schwitrs/xplor/eginput/relaxRatio/dock_rrp.py
(you can remove the relaxation data stuff, if it doesn't apply).
In general, the Vgyr term is safer (than Rgyr) to use on nonglobular
proteins. An example of it's use can be found here:
/home/schwitrs/xplor/eginput/gb1_rdc/refine.py
However, if you have distance restraints (PREs in your case) you may
not need Vgyr. Anyway, the nonbonded term should prevent the subunits
from overlapping significantly.
Please let me know if you'd like further pointers.
best regards--
Charles
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Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
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