hi Guillermo,
Thank you for your help! in your previous mail you said “to increase the atomic
radii (see the 'repel' argument in initRepel)”. But in the script
“from repelPotTools import create_RepelPot,initRepel
repel = create_RepelPot('repel')
potList.append(repel)
rampedParams.append( StaticRamp("initRepel(repel,use14=False)") )
rampedParams.append( MultRamp(.004, 4, "repel.setScale( VALUE)") )
# nonbonded interaction only between C1' atoms
highTempParams.append( StaticRamp("""initRepel(repel,
use14=True,
scale=0.004,
repel=1.2,
moveTol=45,
interactingAtoms="name P"
)""") )
“
I can not find the terms that stands for “atom radius” and how to “increase the
atomic radii(in intRepel)”.
ps: Only RepelPot has the similar term “rMin”; but when I have looked through
the examples in eginput, I did not find the similar use of “RepPot”.
Thank you !
Best,
Yikan
Ph. D candidate
TsingHua University
School of life Sciences
Beijing, China
tel:010-62773783
> 在 2017年12月12日，下午11:38，Bermejo, Guillermo (NIH/CIT) [E]
> <[email protected]> 写道：
>
> Hi Yikan,
>
> I think using Monte Carlo (in the torsion angle randomization) is
> appropriate.
>
> Good luck,
>
> Guillermo
>
>
>
>
>
> From: ZhangYikan <[email protected]>
> Sent: Monday, December 11, 2017 6:36 PM
> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> Subject: Re: [Xplor-nih] Wrong topology structures in conformational sampling
>
> hell Guillermo,
> By the way, although I have known that the comformational sampling problem
> has been an untrival problem util now; how can I make sure that I have
> sampled almost all possible conformations of this RNA?
>
> Yikan
> Ph. D candidate
> TsingHua University
> School of life Sciences
> Beijing, China
> tel:010-62773783
>
>
>
> > 在 2017年12月12日，上午7:25，ZhangYikan <[email protected]> 写道：
> >
> > hello Guillermo,
> > Thank you for your scripts, I have tried it. I found that there are still
> > some wrong topology structures and clahes(some overlaps):1) I will try to
> > fix the repel parameter and rerun the script;
> > 2) in the outputs of the previous zp_0-3.py, I found the terms of “impr”
> > seems unusual(in the .viols), did you have some tools to analysis this
> > energy term ?
> >
> > Thank you!
> > Best,
> >
> > Yikan
> > Ph. D candidate
> > TsingHua University
> > School of life Sciences
> > Beijing, China
> > tel:010-62773783
> >
> >
> >
> >> 在 2017年12月12日，上午2:00，Bermejo, Guillermo (NIH/CIT) [E]
> >> <[email protected]> 写道：
> >>
> >> Hi Yikan,
> >>
> >> I notice that your script seems to be more complicated than it has to be.
> >> I'm not sure this will solve your problem, but I'm attaching a simpler
> >> script based on eginput/rna/fold.py. It's basically the script used to
> >> fold an RNA molecule from an extended conformation (described in the paper
> >> I mentioned before). I modified it so that you load your input pdb
> >> structure and define the different rigid bodies (look for the lines with
> >> an inline comment "# COMPLETE !", where you must enter the right
> >> information). Then, it does torsion angle dynamics using the remaining
> >> torsional degrees of freedom (i.e., at the linker(s)).
> >>
> >> I commented all the experimental restraints. If you want to have the
> >> radius of gyration term (which appears in your script), you can introduce
> >> it yourself. Also, you might want to use it as a starting point for more
> >> complicated stuff, like "breaking" the linkers and randomizing the
> >> position of the domains.
> >>
> >> A suggestion to try to avoid (and detect) knotted structures is to
> >> increase the atomic radii (see the 'repel' argument in initRepel).
> >>
> >> Best,
> >>
> >> Guillermo
> >>
> >> From: ZhangYikan <[email protected]>
> >> Sent: Monday, December 11, 2017 10:43 AM
> >> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> >> Subject: Re: [Xplor-nih] Wrong topology structures in conformational
> >> sampling
> >>
> >> hello Guillermo,
> >>
> >> I want these domains move (as rigid body)randomly and freely to sample all
> >> possible conformations of the RNA.
> >>
> >> Yikan
> >> Ph. D candidate
> >> TsingHua University
> >> School of life Sciences
> >> Beijing, China
> >> tel:010-62773783
> >>
> >>
> >>
> >>> 在 2017年12月11日，下午11:27，Bermejo, Guillermo (NIH/CIT) [E]
> >>> <[email protected]> 写道：
> >>>
> >>> Hi Yikan,
> >>>
> >>> Can you tell me what you are trying to do?
> >>>
> >>> Best,
> >>>
> >>> Guillermo
> >>>
> >>>
> >>> From: ZhangYikan <[email protected]>
> >>> Sent: Friday, December 8, 2017 6:56 PM
> >>> To: Bermejo, Guillermo (NIH/CIT) [E]; [email protected]
> >>> Subject: Re: [Xplor-nih] Wrong topology structures in conformational
> >>> sampling
> >>>
> >>> hi Guillermo,
> >>> yes, i have received your last mails. And the attachment is my scripts.
> >>>
> >>>
> >>> Yikan
> >>> Ph. D candidate
> >>> TsingHua University
> >>> School of life Sciences
> >>> Beijing, China
> >>> tel:010-62773783
> >>>
> >>>
> >>>
> >>>> 在 2017年12月9日，上午12:43，Bermejo, Guillermo (NIH/CIT) [E]
> >>>> <[email protected]> 写道：
> >>>>
> >>>> Hi Yikan,
> >>>>
> >>>> I realized that my original response was only sent to you and not
> >>>> included in the mailing list. Here it is.
> >>>>
> >>>> One possibility is that there's something wrong with your script(s).
> >>>>
> >>>> I recommend basing your calculations on the scripts found in eginput/rna
> >>>> directory (within your Xplor-NIH directory). There you'll find:
> >>>>
> >>>> * fold.py, for initial calculations starting from an extended
> >>>> conformation.
> >>>> * refine.py, for subsequent refinement.
> >>>>
> >>>> In addition, you'll find all the restraints for an example system, in
> >>>> case you want to play with the scripts before venturing into your data.
> >>>> The scripts are highly commented, which should help in customizing them
> >>>> for your needs. There's also a paper describing them [Bermejo et al.,
> >>>> 2016, Structure 24, 806-815].
> >>>>
> >>>> Best,
> >>>>
> >>>> Guillermo
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> From: [email protected]
> >>>> <[email protected]> on behalf of ZhangYikan
> >>>> <[email protected]>
> >>>> Sent: Friday, December 8, 2017 6:53 AM
> >>>> To: [email protected]
> >>>> Subject: [Xplor-nih] Wrong topology structures in conformational sampling
> >>>>
> >>>>
> >>>>
> >>>> hello all,
> >>>>
> >>>> Recently, I am doing conformational sampling with Xplor-NIH. And I got
> >>>> many pdbs, but when I check them I found that some pdbs have wrong
> >>>> topology structures like the attachments(in the pink cycle ): The RNA
> >>>> linker did not run with the right way and It went through the helix. I
> >>>> have tried to pick the structures by the “total energy” or “repel”
> >>>> terms, but it make no sense. Are there someone know how to kick out
> >>>> these wrong structures or to void these errors in the sampling process?
> >>>> Thank you!
> >>>> Yikan
> >>>> Ph. D candidate
> >>>> TsingHua University
> >>>> School of life Sciences
> >>>> Beijing, China
> >>>> tel:010-62773783
> >>
> >> <fold.py>
> >
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