[Chimera-users] Parse error in reply log

Dr. Samson Soon samson at iukl.edu.my
Mon Oct 23 18:08:53 PDT 2017


Dear Dr. Elaine

Thank you so much for your generous insights. As you probably know, I'm
very new to all these. I'm trying to simulate the results of a published
work using autodock vina & other docking systems on RNA aptamers (
https://www.nature.com/articles/srep21285). The binding affinities of the
RNA ligands were predicted and scored using these approaches. I'm surprised
as autodock vina was featured prominently in their report for all virtual
docking experiments analyzed. I will follow up on your
suggestions and compare the outcome. Thanks again for your kind help.

Best regards

*DR. SAMSON SOON I** Director*

*Research Management Center (RMC)*

Infrastructure University Kuala Lumpur (IUKL)

Office: +603.8738.3388 ext 374

Mobile: +6016.221.8010

www.IUKL.edu.my <http://www.iukl.edu.my/> l myIUKL
<https://www.facebook.com/myIUKL> l @myIUKL <https://twitter.com/myIUKL>






On Tue, Oct 24, 2017 at 2:07 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Samson,
> I do not think you can use this tool for what you want to do.  Your
> “ligand” is an RNA, large, with many rotatable bonds.  The Autodock Vina
> web service accessed by Chimera only allows a very small amount of
> sampling, even for a small organic molecule (like a drug) and I do not
> think you would be able to get any scientifically meaningful results on
> this protein-RNA system.
>
> I don’t even know if Vina is meant for protein-RNA docking… if so, you
> would need to download it yourself (to allow adjusting more parameters and
> increasing the sampling higher than what the web service allows). Here is
> the Autodock Vina website, for download and for asking questions about the
> program:
> <http://vina.scripps.edu/>
>
> If you only want an easy web-service approach instead of installing the
> docking program yourself, it might be possible with the Hex server or
> HADDOCK, but I haven’t tried these myself and don’t know if they work with
> protein-RNA either:
>
> Hex
> <http://hexserver.loria.fr/>
>
> HADDOCK (requires registration)
> <http://milou.science.uu.nl/services/HADDOCK2.2/>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Oct 23, 2017, at 10:43 AM, Dr. Samson Soon <samson at iukl.edu.my>
> wrote:
> >
> > Dear Dr. Elaine
> >
> > Thank you so much for your kind advice. I would be very grateful if you
> could test the ligand file (E4) I’m using to dock  with 1sjo to see if the
> parse error persist. I will be following your advice closely & hope it
> solves the problem. Appreciate a lot your kind input in this matter.
> >
> > Best regards
> > Samson Soon, Ph.D
> > Infrastructure University Kuala Lumpur
> > Malaysia.
> >
> > Sent from Mail for Windows 10
> >
> > From: Elaine Meng
> > Sent: Tuesday, 24 October, 2017 12:14 AM
> > To: Dr. Samson Soon
> > Cc: chimera-users at cgl.ucsf.edu
> > Subject: Re: [Chimera-users] Parse error in reply log
> >
> > Dear Samson,
> > I included what you sent as plain text below so that other people can
> see it without using Word.
> >
> > It’s not possible to tell exactly what happened unless we have your
> ligand file to test, since the error is something about the ligand
> hydrogens.  However, one thing you might try in Chimera is to delete all
> the hydrogens and then add them back before running the Audock Vina tool,
> for example, commands:
> >
> > delete H
> > addh
> >
> > Also please understand that Autodock Vina is running on a web service
> outside of Chimera, so the messages in the log are from that separate
> program (not from Chimera directly); in other words, I don’t have any
> deeper understanding of the messages, I can only repeat what it says in the
> log.  Besides the ligand hydrogen error, there is also a warning that your
> search box is very large, so you may want to make that box smaller.  It
> says “see FAQ” which is the Autodock Vina FAQ at Scripps:
> > <http://vina.scripps.edu/manual.html#faq>
> >
> > You do not need to make the box go around the whole receptor, only
> around the possible binding site.
> >
> > I tried docking some simple test ligand of my own against 1sj0, the same
> receptor you were using, and it ran without any problems.
> >
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Chimera(X) team
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> > > On Oct 23, 2017, at 5:13 AM, Dr. Samson Soon <samson at iukl.edu.my>
> wrote:
> > >
> > > Dear experienced chimera users,
> > > I’m constantly failing my auto docking experiments due to the problem
> attached.  Solution to this problem is urgently required. Thank you for any
> kind assistance rendered.
> > > Best regards
> > > Samson
> > >
> > > <Running AutoDock Vina for 1sj0.docx>
> > > _______
> > > Running AutoDock Vina for 1sj0.pdb failed; see Reply Log for more
> information
> > > Application stderr
> > > -----
> > > Parse error on line 124 in file "ligand.pdbqt": ATOM syntax incorrect:
> "Ho" is not a valid AutoDock type. Note that AutoDock atom types are
> case-sensitive.
> > > -----
> > > Application stdout
> > > -----
> > > #################################################################
> > >
> > > # If you used AutoDock Vina in your work, please cite:          #
> > > #                                                               #
> > > # O. Trott, A. J. Olson,                                        #
> > > # AutoDock Vina: improving the speed and accuracy of docking    #
> > > # with a new scoring function, efficient optimization and       #
> > > # multithreading, Journal of Computational Chemistry 31 (2010)  #
> > > # 455-461                                                       #
> > > #                                                               #
> > > # DOI 10.1002/jcc.21334                                         #
> > > #                                                               #
> > > # Please see http://vina.scripps.edu for more information.      #
> > > #################################################################
> > >
> > > WARNING: The search space volume > 27000 Angstrom^3 (See FAQ)
> > > Detected 4 CPUs
> > > Reading input ... -----
> >
> > <E4.pdb>_______________________________________________
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>
>
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