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Hello Jie-rong--
>
> The averaged Q-factors didn't change with the increasing conformers of
> spin-label sites ("ALTs"), so I started the calculation with multi-conformer
> proteins.
so you're using a single conformer of the spin-label?
> In the case of 5-conformer (5 identical polypeptides randomized at high
> temperature without interacting each other) calcualtion, lots of violations
> came out after "pins.showRestraint(0)".
showRestraints(0) always prints out all restraints. You should look at
the rms values for the pre terms. What is the rmsd difference between
the 1-conformer and 2-conformer calculations?
>
> Besides, here are some other questions:
> The following message shown on x-term window and calculation stopped usually
> at 58th or 59th structure (loop); the loop in script was sep up as 64.
> ####
> xplor(22755) malloc: *** vm_allocate(size=754978816) failed (error code=3)
> xplor(22755) malloc: *** error: can't allocate region
> xplor(22755) malloc: *** set a breakpoint in szone_error to debug
> Exception exceptions.AttributeError: "'NoneType' object has no attribute
> 'settrace'" in <bound method XplorSimulationPtr.__del__ of <C XplorSimulation
> instance at _80312103_p_XplorSimulation>> ignored
> ####
I would guess this is a memory leak- probably in the PRE term. Is a core
file created?
>
> The "funType" (e.g. "harmonic") is not specified in the script. Is it because
> that the type of penalty function is defaulted? (not described in the prePot
> manual as well.)
harmonic is default- I've added that to the documentation. thanks.
>
> How many "npc" should be set-in? My starting structure contains 8 cycteine
> mutation cites, while the restraint tables (e.g. k6c.tbl, s20c.tbl...) are
> read in one by one. What's the role of "npc" in calculation?
>
- From what I can tell, npc is the number equivalent spin labels- this is
used for homodimers in which both subunits are labeled. Since your sites
are not equivalent, you shoudl set npc=1. npc scales the calculated pre
values.
hope this helps--
Charles
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