ADL: "pdbcen" function

Antonio Cavazzuti acavazzuti at ipb.csic.es
Thu Mar 13 10:13:36 PDT 2008


Thank you very much Tee for the answer. 
The solution that you send me did not fix the problem. I ask to you a little
more patience..:)
I looked for pdbcen in my PC (find / -name pdbcen), but there is no file with
this name in the hard disk (just the link created with "ln -s
/usr/local/dist305/share/pdbcen pdbcen" in /usr/local/bin ) . 
Also I do not have /dist305 folder. Googleing "/dist305" I found only links to
Autodock3.* releases. Maybe the fact that I am using Autodock4 Autogrid4 and
ADT 1.5 (under Ubuntu 7.10) is part of the problem.. maybe an incomplete
installation..
Thank you one more time,
Antonio



> Message: 6
> Date: Wed, 12 Mar 2008 05:30:38 +0000 (GMT)
> From: Tee Pioj <tee_piorj at yahoo.com>
> Subject: Re: ADL: "pdbcen" function
> To: autodock at scripps.edu
> Message-ID: <447550.48503.qm at web59311.mail.re1.yahoo.com>
> Content-Type: text/plain; charset=us-ascii
> 
> Hello, Antonio Cavazzuti 
> Again you  should solve this problem with these command:
> 
> $cd /usr/local/bin
> 
> and then
> 
> $ln -s /usr/local/dist305/share/pdbcen pdbcen
> 
> This commamd is a link command (ln). This put link of pdbcen command 
> into bin directory. Try typing pdbcen again. It gonna work.
> 
> Best luck,
> Tee Piroj
> 
> ----- Original Message ----
> From: Antonio Cavazzuti <acavazzuti at ipb.csic.es>
> To: autodock at scripps.edu
> Sent: Tuesday, March 11, 2008 10:21:16 PM
> Subject: ADL: "pdbcen" function
> 
> Hi,
> I am using Autodock4 Autogrid4 and ADT 1.5 under Ubuntu. I had 
> problems with grid setting up. Tee Piroj (thanks you!!) previously 
> suggested me to use "pdbcen" command to obtain center of binding 
> site and put them in grid dialogue box. Finally I had to manually 
> calculate center of binding site because "pdbcen" doesn't work.. I 
> open a terminal windows, I change directory where my pdb file is and 
> I enter
> 
> pdbcen myfile.pdb
> 
> ....but the answer is "command not found"
> 
> How can I solve this? 
> Thanks in advance,
> Antonio
> 
> Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
> Avda. Conocimiento S/N
> Parque Tecnologico Ciencias de la Salud
> 18100 Armilla - GRANADA
> Spain
> Tlf: 958181621
> Fax: 958181632
> http://www.ipb.csic.es?wp_ml=0
> --
> 
> ________________________________________________
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> 
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> ------------------------------
> 
> Message: 7
> Date: Tue, 11 Mar 2008 22:34:59 -0700 (PDT)
> From: sargis at scripps.edu
> Subject: Re: ADL: ADT problems on Mac OS 10.5 and Leopard
> To: autodock at scripps.edu
> Message-ID:
> 	<3476.71.138.63.235.1205300099.squirrel at webmail.scripps.edu>
> Content-Type: text/plain;charset=iso-8859-1
> 
> > Hi Sargis,
> >
> > Thanks a ton for pointing me to the Cjmart site. I downloaded and
> > installed
> > the x11 package. By dafault it got installed in /usr/X11R6 folder. I then
> > renamed the X11R6 folder to X11. Then per instructions on
> > http://aaroniba.net/articles/x11-leopard.html?wp_ml=0, following step 3, I
had to
> > change the "exec quartz-wm" statement in xinitrc.
> >
> > Should the line be changed to: "exec /usr/X11/bin/quartz-wm".....though
> > the
> > instruction says "exec /usr/X11R6/bin/quartz-wm". I do not have a X11R6
> > folder under /usr now.
> >
> > What did you do? Do I need to anything else? Please advise.
> 
> Hi Lakshmi,
> 
> I did change xinitrc, however you can make a link or hard copy of /usr/X11
> as /usr/X11R6 so that either way it works. Just make sure that you 
> can start X11.app.
> 
> Sargis
> 
> ------------------------------
> 
> Message: 8
> Date: Wed, 12 Mar 2008 11:18:49 +0530
> From: "lakshmi ganesan" <lakshmi.g85 at gmail.com>
> Subject: Re: ADL: ADT problems on Mac OS 10.5 and Leopard
> To: autodock at scripps.edu
> Message-ID:
> 	<cbb32e2e0803112248x6c0c170dhd53cd836717737cc at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Thank you, Sargis. Will try that. So you changed the line in xinitrc
> to  "exec /usr/X11/bin/quartz-wm", right?
> 
> Will keep you posted.
> 
> Regards, Lakshmi
> 
> On 3/12/08, sargis at scripps.edu <sargis at scripps.edu> wrote:
> >
> > > Hi Sargis,
> > >
> > > Thanks a ton for pointing me to the Cjmart site. I downloaded and
> > > installed
> > > the x11 package. By dafault it got installed in /usr/X11R6 folder. I
> > then
> > > renamed the X11R6 folder to X11. Then per instructions on
> > > http://aaroniba.net/articles/x11-leopard.html?wp_ml=0, following step 3,
I had
> > to
> > > change the "exec quartz-wm" statement in xinitrc.
> > >
> > > Should the line be changed to: "exec /usr/X11/bin/quartz-wm".....though
> > > the
> > > instruction says "exec /usr/X11R6/bin/quartz-wm". I do not have a X11R6
> > > folder under /usr now.
> > >
> > > What did you do? Do I need to anything else? Please advise.
> >
> > Hi Lakshmi,
> >
> > I did change xinitrc, however you can make a link or hard copy of /usr/X11
> > as /usr/X11R6 so that either way it works. Just make sure that you can
> > start X11.app.
> >
> > Sargis
> >
> > ________________________________________________
> > --- ADL: AutoDock List  ---
http://autodock.scripps.edu/mailing_list?wp_ml=0 ---
> >
> 
> ------------------------------
> 
> Message: 9
> Date: Wed, 12 Mar 2008 14:35:52 +0530
> From: "Richa Batra" <richa.batra at gmail.com>
> Subject: ADL: How to view docked complex?
> To: autodock at scripps.edu
> Message-ID:
> 	<b999f90c0803120205n6d9461deyf33cbb87e1834959 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Dear All
> I have got some dlg files. n there are some 100 trials for each of 
> them so i have 100 docked conformations. can anyone please tell me 
> how to visualize these docked conformations.
> 
> Regards
> Ms Richa Batra
> Bioinformatics Centre,
> Universtiy of Pune,
> Pune, MHT, India.
> Alt. Id: batra.richa at yahoo.com
> 
> ------------------------------
> 
> Message: 10
> Date: Wed, 12 Mar 2008 18:56:48 +0100
> From: "miriam sgobba" <miriam.sgobba at gmail.com>
> Subject: ADL: increasing the grid points number
> To: autodock at scripps.edu
> Message-ID:
> 	<4ea94de60803121056j6d481e77x6d5f89e1a744c8d6 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi all,
> I would like to built a grid with a number of points higher than 126 
> x 126 x 126 and a spacing of 0.375 using AutoDock4. To this end, I 
> read that I must modify the number in the MAX_GRIDS_PTS line of the 
> autocomm.h file (in the src/autodock/ directory) and then I re-
> compile autogrid. Is this a right operation? What does this 
> operation implies? Can this operation cause problems of swapping or memory?
> Does anyone use a grid with these parameters?
> 
> Appreciate any help.
> 
> Thank you very much in advance.
> Miriam
> 
> ------------------------------
> 
> ________________________________________________
> --- ADL: AutoDock List  ---
http://www.scripps.edu/pub/olson-web/doc/autodock/?wp_ml=0 ---
> 
> End of autodock Digest, Vol 48, Issue 17
> ****************************************


Instituto de Parasitologia y Biomedicina "Lopez-Neyra"
Avda. Conocimiento S/N
Parque Tecnologico Ciencias de la Salud
18100 Armilla - GRANADA
Spain
Tlf: 958181621
Fax: 958181632
http://www.ipb.csic.es
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