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

John J. Irwin jji at cgl.ucsf.edu
Wed Mar 18 10:07:31 PDT 2009


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>


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