[Dock-fans] Re: Dock-fans Digest, Vol 6, Issue 9

Gareth Williams gareth.2.williams at kcl.ac.uk
Wed Apr 20 06:16:15 PDT 2005


Problem with molcharge solved. An extra line has to be inserted before the 
@<TRIPOS>ATOM line in the mol2 file. Otherwise DOCK GRID won't process the 
mol2 file.


At 12:00 19/04/2005 -0700, you wrote:
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>Today's Topics:
>
>    1. sphgen problem on OS X (Sebastien Gerega)
>    2. Re: sphgen problem on OS X (Terry Lang)
>    3. (no subject) (Gareth Williams)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Tue, 19 Apr 2005 10:08:18 +1000
>From: Sebastien Gerega <sger3477 at mail.usyd.edu.au>
>Subject: [Dock-fans] sphgen problem on OS X
>To: dock-fans at docking.org
>Message-ID: <1113869298.42644bf26dfae at www-mail.usyd.edu.au>
>Content-Type: text/plain; charset=ISO-8859-1
>
>I am attempting to use the sphgen binary distributed with the Mac version
>of DOCK 5.2 but am getting the following error:
>exit
>dyld: /Users/downmac/Desktop/Sebastien/DOCK/dock.5.2_mac/bin/sphgen can't
>open library: /usr/local/lib/libg2c.0.dylib  (No such file or directory,
>errno = 2)
>Trace/BPT trap
>
>Has anyone else had this problem and know how to deal with it?
>
>Also, I am aware from a previous dock-fans message that using DOCK for
>protein-protein docking is not a current area of research. However, it
>does have the capability to do so and I am wondering whether there is
>anyone out there taht uses it for that application that I could ask some
>questions?
>
>thanks,
>Sebastien
>
>----------------------------------------------------------------
>This message was sent using IMP, the Internet Messaging Program.
>
>
>------------------------------
>
>Message: 2
>Date: Mon, 18 Apr 2005 17:54:22 -0700
>From: Terry Lang <terry at cgl.ucsf.edu>
>Subject: Re: [Dock-fans] sphgen problem on OS X
>To: Sebastien Gerega <sger3477 at mail.usyd.edu.au>,
>         dock-fans at docking.org
>Message-ID: <6.1.1.1.2.20050418174849.025e32c0 at socrates.cgl.ucsf.edu>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>Dear Sebastien,
>
>    The sphgen code was compiled on the Mac OS X using a g77 compiler, which
>it looks like you do not have.  You have two options:  1)  you can
>recompile sphgen (and probably all of the other executables) using the
>compiler you have installed on your computer or 2) you can install the gcc
>and g77 compilers on your system (for more information, go to
>http://www.gnu.org/home.html).
>
>Sincerely,
>Terry
>
>
>At 05:08 PM 4/18/2005, Sebastien Gerega wrote:
> >I am attempting to use the sphgen binary distributed with the Mac version
> >of DOCK 5.2 but am getting the following error:
> >exit
> >dyld: /Users/downmac/Desktop/Sebastien/DOCK/dock.5.2_mac/bin/sphgen can't
> >open library: /usr/local/lib/libg2c.0.dylib  (No such file or directory,
> >errno = 2)
> >Trace/BPT trap
> >
> >Has anyone else had this problem and know how to deal with it?
> >
> >Also, I am aware from a previous dock-fans message that using DOCK for
> >protein-protein docking is not a current area of research. However, it
> >does have the capability to do so and I am wondering whether there is
> >anyone out there taht uses it for that application that I could ask some
> >questions?
> >
> >thanks,
> >Sebastien
> >
> >----------------------------------------------------------------
> >This message was sent using IMP, the Internet Messaging Program.
> >_______________________________________________
> >Dock-fans mailing list
> >Dock-fans at docking.org
> >http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
>***NOTE:  This is a new e-mail address (terry at cgl.ucsf.edu)  Please update
>your address book!***
>
>P. Therese (Downing) Lang
>Kuntz and James Labs
>UCSF - CCB Graduate Program
>Phone:  (415)476-3986
>
>
>
>------------------------------
>
>Message: 3
>Date: Tue, 19 Apr 2005 17:22:16 +0100
>From: Gareth Williams <gareth.2.williams at kcl.ac.uk>
>Subject: [Dock-fans] (no subject)
>To: dock-fans at docking.org
>Message-ID: <5.2.0.9.0.20050419171905.01c1f2e8 at mail.kcl.ac.uk>
>Content-Type: text/plain; charset="us-ascii"; format=flowed
>
>I'm running my first DOCK project. The receptor file was converted from pdb
>to mol2 format with the openeye molcharge application e.g. molcharge
>file.pdb file.mol2
>
>However, when running GRID I get the following error:
>
>Unable to find ATOM record for ***** in file.mol2 Error reading in receptor
>
>Any suggestions?
>
>
>Gareth Williams
>Wolfson CARD
>The Wolfson Wing
>Hodgkin Building
>Kings College London
>London SE1 1UL
>Tel:  020 7848 6806
>Fax: 020 7848 6816
>http://www.kcl.ac.uk/depsta/biomedical/CARD/CARD.htm
>
>
>
>
>------------------------------
>
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>
>End of Dock-fans Digest, Vol 6, Issue 9
>***************************************

Gareth Williams
Wolfson CARD
The Wolfson Wing
Hodgkin Building
Kings College London
London SE1 1UL
Tel:  020 7848 6806
Fax: 020 7848 6816
http://www.kcl.ac.uk/depsta/biomedical/CARD/CARD.htm





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