[Dock-fans] vdw parameters for Selenium

Zhong, Shijun szhong at rx.umaryland.edu
Thu Sep 17 14:12:30 PDT 2009


Hello there,

Could anybody give a set of vdw parameters for Se (Selenium)?
Right now, I am using the parameters for S (Sulfur) to compute Se.
---------------------------------------
name            Selenium
atom_model      either
radius          2.000
well_depth      0.250
heavy_flag      1
valence         6
gbradii         1.80
gbscale         0.96

definition      Se
---------------end-------------------


Thanks!

Shijun

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Sent: Thursday, September 17, 2009 3:00 PM
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Subject: Dock-fans Digest, Vol 64, Issue 9

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Today's Topics:

   1. ubuntu yacc;      was Re: [Fwd: Re: Your DOCK 6 license has been
      approved] (Scott Brozell)
   2. ubuntu faq; was Re: dock6 (Scott Brozell)
   3. Fwd:  ubuntu faq; was Re: dock6 (Davide Mercadante)


----------------------------------------------------------------------

Message: 1
Date: Wed, 16 Sep 2009 15:37:09 -0400
From: Scott Brozell <sbrozell at rci.rutgers.edu>
Subject: [Dock-fans] ubuntu yacc;       was Re: [Fwd: Re: Your DOCK 6
        license has been approved]
To: St?phane Ransac <stephane.ransac at u-bordeaux2.fr>
Cc: dock-fans at docking.org
Message-ID: <20090916193709.GA10808 at casegroup.rutgers.edu>
Content-Type: text/plain; charset=iso-8859-1

Hi,

On Wed, Sep 16, 2009 at 05:31:41PM +0200, St?phane Ransac wrote:
>
> Thank you for your message. I just download dock 6.3 and try to install it on my computer (ubuntu 9.04).
>
> Make dock    works even if I got a lot of warning message.
>
> However, make utils leads to an error :
>
> ...
> gcc -c -O2 -DSYSV variables.c
> yacc parser.y
> make[2]: yacc: Command not found
> make[2]: *** [parser.c] Error 127
> make[2]: Leaving directory `/home/ransac/dock6/src/tleap'
> make[1]: *** [utils] Error 2
> make[1]: Leaving directory `/home/ransac/dock6/src'
> make: *** [utils] Error 2
>
>
> I try to look for a "yacc" command or program but I did not found it. Since I'm still a novice in unix system, I do not know how to solve it.
>

The story is here:
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#yacc:Commandnotfound

The ubuntu fix is
sudo apt-get install byacc
Then
which yacc
should emit
/usr/bin/yacc

Rebuild via:
cd install
make utils
make test

Scott



------------------------------

Message: 2
Date: Wed, 16 Sep 2009 22:41:31 -0400
From: Scott Brozell <sbrozell at rci.rutgers.edu>
Subject: [Dock-fans] ubuntu faq; was Re: dock6
To: vamsi krishna <vamsi at nus.edu.sg>
Cc: dock-fans at docking.org
Message-ID: <20090917024130.GB10808 at casegroup.rutgers.edu>
Content-Type: text/plain; charset=us-ascii

Hi,

On Wed, Sep 09, 2009 at 10:28:54AM -0700, John J. Irwin wrote:
>
> We are sorry you are having problems with DOCK on ubuntu.
>
> vamsi krishna wrote:
> >                      Thank you for providing wonderful tool for
> > docking. as i am  using ubuntu linux, i could not install previous
> > version (dock 6.2). I could not get any assistance for even community
> > regarding this issue.  I am not sure why it is so please help me to
> > sort out the problem ( any prerequisites need to  be installed or
> > something like that ) . I hope i may be successful with new release
> > dock 6.3 . So tried to download it but could not find any link.

http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#ubuntu

Scott



------------------------------

Message: 3
Date: Thu, 17 Sep 2009 15:12:36 +1200
From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
Subject: [Dock-fans] Fwd:  ubuntu faq; was Re: dock6
To: dock-fans <dock-fans at docking.org>
Message-ID:
        <1da69e140909162012v77c01540vb08241d0005a6455 at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi to all the community,

please see the mail forwarded if you are interested in installing DOCK on an
ubuntu operative machine.

Cheers,
Davide

---------- Forwarded message ----------
From: Davide Mercadante <dmer018 at aucklanduni.ac.nz>
Date: 2009/9/17
Subject: Re: [Dock-fans] ubuntu faq; was Re: dock6
To: Scott Brozell <sbrozell at rci.rutgers.edu>


Hi!,

I have successfull installed dock (6.2) on an ubuntu linux machine 9.04, and
unfortunately not without difficulties.
First thing you need to install:

build-essential
byacc

as explained on the DOCK website in the FAQ section:
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#ubuntu

Then:
in the version 6.2 of DOCK there were some heading missing in some of the
files .cpp present in the folder dock6/src/dock. You need to insert these
headings...I sent an e-mail to the community prevoiously specifying whose
files that need to be modified.
You can find my suggestions here:

http://blur.compbio.ucsf.edu/pipermail/dock-fans/2009-May/002077.html

I don't know if in the 6.3 release these header missing problems have been
solved.
In addition, after the command ./configure "gnu" open the file config.h
created by the configure script and change the name of fortran compiler from
f77 to gfortran.
This actually is needed because in ubuntu f77 is not released and there are
problems of dependencies if you try to install it. Gfortran works fine and
dock will be compiled without problems.

On my ubuntu machine DOCK 6.2 worked perfectly.
Hope this can help who has got problems installing DOCK on an ubuntu
machine.

Cheers,
Davide

Davide Mercadante - PhD Student -
The University of Auckland
Department of Chemistry - Computational Chemistry Division -
Auckland
New Zealand

2009/9/17 Scott Brozell <sbrozell at rci.rutgers.edu>

Hi,
>
> On Wed, Sep 09, 2009 at 10:28:54AM -0700, John J. Irwin wrote:
> >
> > We are sorry you are having problems with DOCK on ubuntu.
> >
> > vamsi krishna wrote:
> > >                      Thank you for providing wonderful tool for
> > > docking. as i am  using ubuntu linux, i could not install previous
> > > version (dock 6.2). I could not get any assistance for even community
> > > regarding this issue.  I am not sure why it is so please help me to
> > > sort out the problem ( any prerequisites need to  be installed or
> > > something like that ) . I hope i may be successful with new release
> > > dock 6.3 . So tried to download it but could not find any link.
>
> http://dock.compbio.ucsf.edu/DOCK_6/faq.htm#ubuntu
>
> Scott
>
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
>
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