Hello Yikan--
> Thank you for your sincerely help! Now, I am trying to find an
> appropriate repel value. But I have two questions about Xplor-NIH:
> 1) About random seed:"the same seed number on the same computer
> yields the same results” In oder to generate more structures, I have
> submitted many jobs to the cluster. like “ #!/bin/sh
>
> #8st job
> k=8
> cd /Share/home/fangxy/Users/Zhangyk/Zxplor-test/Gwnvpks/sec_wp/secout/8
>
> xplor -py ../../wp.py ../../${k}.pdb”
> in these jobs, the random seeds in the “wp.py” are all the same, so
> I do not know whether this will effect the results of the
> conformational sampling.
This is a problem: since the calculations all have the same seed, they
should all yield the same result. One solution is to remove the
argument to protocol.initRandomSeed() - then the seed will be
initialized using the current second. As long as the programs are
started more than a second apart, the different runs will utilize
difference seeds. Otherwise you will need to construct scripts which
differ by the seed (or take an argument specifying the seed).
The -parallel, pbsxplor and slurmXplor facilities all take care of
this for you.
>
> 2) “https://link.springer.com/protocol/10.1007/978-1-4939-7386-6_14” mentioned
> that “def calcOneStructure(loopInfo):” is consist of “High Temperature Stage”
> “Simulated Annealing Stage” “Torsion Angle Minimization” and so on. One
> simulate
> annealing stage(temp from 3500 to 25) will calculate only one structure. And
> when
> I checked the output pdb, I found that the two outputs of adjacent
> numbers(like
> 1.pdb, 2.pdb) only have a little similarity and that is OK for the sampling.
> So
> if we want to sampling more conformations, do we have some other parameter to
> adjust (in the three stages) ?
This should be sufficient, except for the case of docking two
non-covalently bound domains, in which case an extra
domain-randomization step is necessary.
> And do the numberOfStructures has "upper limit” ?
Only limits of memory and storage space.
best regards--
Charles
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