[Zinc-fans] the number of molecules in the mol2 file is not enough!

CAI Qixu caiqixu at gmail.com
Thu Mar 26 07:45:56 PDT 2009


Hi John,
Yes, I have found the file splitmol.h in legacy accessories, but I don't
kown how to use .f files. Does it need to complie? Could you tell me how to
use splitmol?
Thank you very much. Good luck!

Qixu Cai
Email: caiqixu at gmail.com


On Thu, Mar 19, 2009 at 1:07 AM, John J. Irwin <jji at cgl.ucsf.edu> wrote:

> Hi CAI Qixu
>
> I wrote that splitmol is in the DOCK accessories package ("legacy
> accessories"), which it is.  I just downloaded it myself to test. Anyone
> with any DOCK license can download it.
>
> Good luck
>
> John
>
>
> CAI Qixu wrote:
> > Thank you. but it seems that splitmol is not in the DOCK package.
> > Shall I need to install something others?
> > Good luck!
> >
> > On Wed, Mar 18, 2009 at 5:17 AM, John J. Irwin <jji at cgl.ucsf.edu
> > <mailto:jji at cgl.ucsf.edu>> wrote:
> >
> >     You can use molchunk.py, if you have OEChem from OpenEye.  If you
> >     don't,
> >     you can use splitmol, which is part of the DOCK accessories package,
> I
> >     believe.
> >
> >
> >
> >     CAI Qixu wrote:
> >     > Hi John,
> >     > Er...Yes, now I have found it. Thank you very much!!!
> >     > Another question: is there some methods to divide the mol2 file to
> >     > several parts? Because I cannot dock it at a time.
> >     > Thank you again.
> >     >
> >     > On Thu, Mar 12, 2009 at 8:41 AM, John J. Irwin <jji at cgl.ucsf.edu
> >     <mailto:jji at cgl.ucsf.edu>
> >     > <mailto:jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>>> wrote:
> >     >
> >     >     Sigma-Aldrich.  No e. Try again, or scroll down to "S" and
> >     look for it
> >     >     there.
> >     >
> >     >
> >     >     CAI Qixu wrote:
> >     >     > Hi John,
> >     >     > At first, i want to download sigma-aldrich in the "by
> >     vendor" page
> >     >     > that you just said, but i cannot find sigma-alderich in
> >     the page for
> >     >     > many times, that is strange! Because in the "search and
> >     browse"
> >     >     page,
> >     >     > the sigma-alderich is exist! Could you tell me why?
> >     >     > Thanks very much!
> >     >     >
> >     >     > On 3/12/09, John J. Irwin <jji at cgl.ucsf.edu
> >     <mailto:jji at cgl.ucsf.edu>
> >     >     <mailto:jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>>> wrote:
> >     >     >
> >     >     >> Hi Qixu
> >     >     >>
> >     >     >> Why don't you try the "download by vendor" page?
> >     >     >> ZINC main page, Subsets menu, "by vendor"
> >     >     >> http://zinc.docking.org/vendor0/
> >     >     >>
> >     >     >> search for Sigma Aldrich, then click on the download button
> >     >     >> http://zinc.docking.org/vendor0/sial/index.html
> >     >     >>
> >     >     >> Downloads are at the bottom of the page.  mol2, single (or
> >     >     usual). or
> >     >     >> just click on the "0" to get the file directly.
> >     >     >>
> >     >     >> let me know if this is not what you wanted.
> >     >     >>
> >     >     >> Good docking
> >     >     >>
> >     >     >> John
> >     >     >>
> >     >     >> CAI Qixu wrote:
> >     >     >>
> >     >     >>> Hi John,
> >     >     >>> I search sigma-aldrich of the vender in the page
> >     >     >>> http://zinc.docking.org/choose.shtml, and download the
> >     table.
> >     >     Though
> >     >     >>> the table, there are 14669 comounds in the table. But when
> I
> >     >     download
> >     >     >>> the mol2 file, there is not enough compounds in the file!?
> >     >     >>> Thank you very much!
> >     >     >>>
> >     >     >>> On Thu, Mar 12, 2009 at 12:37 AM, John J. Irwin
> >     >     <jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>
> >     <mailto:jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>>
> >     >     >>> <mailto:jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>
> >     <mailto:jji at cgl.ucsf.edu <mailto:jji at cgl.ucsf.edu>>>> wrote:
> >     >     >>>
> >     >     >>>     Hi Qixu
> >     >     >>>
> >     >     >>>     Thanks for your email.
> >     >     >>>
> >     >     >>>     CAI Qixu wrote:
> >     >     >>>     > Hi, everyone. I am new to ZINC, and have some
> >     questions
> >     >     about ZINC.
> >     >     >>>     > 1, I download the mol2 file and the table from the
> >     zinc,
> >     >     but I find
> >     >     >>>     > the number of the molecules in the mol2 file is less
> >     >     than the
> >     >     >>>     > molecular number in the table! Why???
> >     >     >>>     If you tell me which subset you downloaded, I will
> >     check.
> >     >      If you send
> >     >     >>>     me the numbers of molecules in each list (off the
> list),
> >     >     that will
> >     >     >>>     save
> >     >     >>>     me time, and help me to answer you more quickly.
> >     >     >>>
> >     >     >>>     Some subsets don't get exported correctly.  When I find
> >     >     these I try to
> >     >     >>>     put them right.  Of course there should be perfect
> >     >     agreement, but
> >     >     >>>     discrepencies under 1% are normal and, using my current
> >     >     protocols,
> >     >     >>>     challenging to avoid. I will look promptly at
> >     differences
> >     >     over 1% and
> >     >     >>>     try to put it right asap.
> >     >     >>>     > 2, Is there some useful methods for calculate the
> >     number
> >     >     of the
> >     >     >>>     > molecules in the mol2 file???
> >     >     >>>     > Thank you very much!!!
> >     >     >>>     grep -c '@<TRIPOS>MOLECULE' *.mol2
> >     >     >>>
> >     >     >>>     John
> >     >     >>>     UCSF ZINC Team
> >     >     >>>
> >     >     >>>
> >     >     >>>
> >     >     >>>
> >     >     >>> --
> >     >     >>> Cai Qixu
> >     >     >>> Email: caiqixu at gmail.com <mailto:caiqixu at gmail.com>
> >     <mailto:caiqixu at gmail.com <mailto:caiqixu at gmail.com>>
> >     >     <mailto:caiqixu at gmail.com <mailto:caiqixu at gmail.com>
> >     <mailto:caiqixu at gmail.com <mailto:caiqixu at gmail.com>>>
> >     >     >>>
> >     >     >
> >     >     >
> >     >
> >     >
> >     >
> >     >
> >     > --
> >     > Cai Qixu
> >     > Email: caiqixu at gmail.com <mailto:caiqixu at gmail.com>
> >     <mailto:caiqixu at gmail.com <mailto:caiqixu at gmail.com>>
> >
> >
> >
> >
> > --
> > Cai Qixu
> > Email: caiqixu at gmail.com <mailto:caiqixu at gmail.com>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://blur.compbio.ucsf.edu/pipermail/zinc-fans/attachments/20090326/6814b099/attachment.html 


More information about the Zinc-fans mailing list