[Zinc-fans] the number of molecules in the mol2 file is not enough!
John J. Irwin
jji at cgl.ucsf.edu
Thu Mar 26 13:45:20 PDT 2009
did you try
make splitmol
or maybe
g77 -o splitmol splitmol.f
?
CAI Qixu wrote:
> 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 <mailto:caiqixu at gmail.com>
>
>
> On Thu, Mar 19, 2009 at 1:07 AM, John J. Irwin <jji at cgl.ucsf.edu
> <mailto: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>
> > <mailto: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>>
> > > <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:
> > >
> > > 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>>
> > > <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
> > > >>
> > > >> 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>>>
> > > >>> <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 <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>>>
> > > <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 <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>>
> > <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>>
>
>
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