From owner-chemistry@ccl.net Tue Feb 7 06:45:00 2006 From: "D.BIO- Gerard Pujadas gerard.pujadas{:}urv.net" To: CCL Subject: CCL: Is there any tool for converting ligand structures in AutoDock format? Message-Id: <-30803-060207064238-16738-BQi/b3kuMDxR9NvKKt1zxA###server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Tue, 7 Feb 2006 12:42:07 +0100 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas^urv.net] Dear members of the CCL list, I wonder if there is any tool that can be used to transform a set of ligand structures (for example, downloaded from the ZINC database) into the format required for its use by AutoDock. With many thanks in advances for your help Yours sincerely, Gerard -- ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== Dr. Gerard Pujadas Grup de recerca en "Vi i Salut" Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas]^[urv.net Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 559597 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Tue Feb 7 08:23:00 2006 From: "Reinaldo Pis Diez pis_diez\a/yahoo.com.ar" To: CCL Subject: CCL: Molekel 4.3 and Fedora Core 4 Message-Id: <-30804-060207060604-14661-sDMiLhjZbGncT7Quy8vwMg() server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Feb 2006 08:07:03 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [pis_diez * yahoo.com.ar] Hi ccl'ers, I'm having trouble with molekel 4.3 (with Mesa libs statically linked) installed on a box with Fedora Core 4. I've made the corresponding symbolic link to avoid the libstdc++-libc6.1-2.so.3 lib error. But when I try to run the program I got the message /usr/local/molekel/bin/molekel4.3.linux-mesa: symbol lookup error: /usr/local/molekel/bin/molekel4.3.linux-mesa: undefined symbol: __builtin_new and it doesn't run of course. Any hints? Thanks in advance. Regards, Reinaldo ___________________________________________________________ 1GB gratis, Antivirus y Antispam Correo Yahoo!, el mejor correo web del mundo http://correo.yahoo.com.ar From owner-chemistry@ccl.net Tue Feb 7 09:15:00 2006 From: "John Hearns john.hearns^_^streamline-computing.com" To: CCL Subject: CCL: Molekel 4.3 and Fedora Core 4 Message-Id: <-30805-060207090948-32293-4rueGL44kDMmBcaj4lb2XA]|[server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 07 Feb 2006 14:09:27 +0000 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns!^!streamline-computing.com] On Tue, 2006-02-07 at 08:36 -0500, Reinaldo Pis Diez pis_dieza/yahoo.com.ar wrote: > > I'm having trouble with molekel 4.3 (with Mesa libs statically > linked) installed on a box with Fedora Core 4. I've made the > corresponding symbolic link to avoid the libstdc++-libc6.1-2.so.3 lib > error. Have you installed the compat-libstdc++ package? That is the way to get those older libraries, rather than making links. From owner-chemistry@ccl.net Tue Feb 7 09:49:00 2006 From: "Yingbin Ge yingbin.ge|-|gmail.com" To: CCL Subject: CCL: ACES Message-Id: <-30806-060207020604-25551-Uj266oTDbnzVBMa5T1DEyw^_^server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary="----=_Part_8115_8630833.1139295956250" Date: Tue, 7 Feb 2006 01:05:56 -0600 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge[#]gmail.com] ------=_Part_8115_8630833.1139295956250 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Thanks Daniel! Yingbin On 2/6/06, Crawford, Daniel crawdad]![vt.edu wrote: > Sent to CCL by: "Crawford, Daniel" [crawdad,vt.edu] > > [The MS "winmail.dat" attachment removed by jkl*ccl.net] > > Use the "DROP_MO" keyword to freeze core orbitals. For example, if you > want to freeze the lowest three orbitals (ordered by energy), you would > set: DROP_MO=3D1>3 > > -Daniel > ------=_Part_8115_8630833.1139295956250 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Thanks Daniel!
 
Yingbin
 
On 2/6/06, C= rawford, Daniel crawdad]![vt.edu <owner-chemistry.:.ccl.net> wrot= e:
Sent to CCL by: "Crawford, = Daniel" [crawdad,vt.edu]

[The MS = " winmail.dat" attachment removed by jkl*ccl.= net]

Use the "DROP_MO" keyword to freeze core orbitals= .  For example, if you
want to freeze the lowest three orbital= s (ordered by energy), you would
set:  DROP_MO=3D1>3

-Daniel
 
------=_Part_8115_8630833.1139295956250-- From owner-chemistry@ccl.net Tue Feb 7 10:42:01 2006 From: "Gilles Marcou gilles.marcou,+,pharma.u-strasbg.fr" To: CCL Subject: CCL: Is there any tool for converting ligand structures in AutoDock format? Message-Id: <-30807-060207094720-20938-YlFieNXJrc2T5kex/YFVSw|-|server.ccl.net> X-Original-From: Gilles Marcou Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 7 Feb 2006 14:49:52 +0100 MIME-Version: 1.0 Sent to CCL by: Gilles Marcou [gilles.marcou!A!pharma.u-strasbg.fr] Hi, I'm not sure if this is what you're searching for... First of all, you should begin with a 3D model of the ligand, with no ambiguities on ionization state and tautomer state. It should be easier to use mol2 format. You should care a lot about atom typing too. In the following I assume you are working on an UNIX/Linux workstation or you have cygwin -or equivalent- installed on your Window$. Then you can use the programs distributed with autodock like deftors. They are interactive but you can answer automatically to the questions using standard shell syntaxe. For example if you have a seperate mol2 for each of your ligand in a specific directory, following the Get Started part of the autodock manual, a bash script would look like: for lig in MyLigandsDir/*.mol2; do $AUTODOCK_DIR/share/deftors $lig < Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas^urv.net] > > Dear members of the CCL list, > > I wonder if there is any tool that can be used to > transform a set of ligand structures (for > example, downloaded from the ZINC database) into > the format required for its use by AutoDock. > > With many thanks in advances for your help > > Yours sincerely, > > Gerard -- Gilles Marcou Université Louis Pasteur de Strasbourg Faculté de Pharmacie Laboratoire de Pharmacochimie de la Communication Cellulaire, UMR7081 74, Route du Rhin, BP24 67401 Illkirch tel.:(0033)(0)3.90.24.42.21 eMail: marcou[A]pharma.u-strasbg.fr From owner-chemistry@ccl.net Tue Feb 7 11:17:00 2006 From: "Ulrike Salzner salzner-x-fen.bilkent.edu.tr" To: CCL Subject: CCL: LINUX system problem Message-Id: <-30808-060207105412-27011-t2Cvz6G9+Ckgl43F5ProHw,+,server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 07 Feb 2006 17:54:06 +0200 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner:+:fen.bilkent.edu.tr] Dear all, we have one PC that is a real lemon. It made problems after about 7 months of usage and crashes very often. One thing that happens is that after crashing, all the file systems have changed their lables by adding a 1. For instance / goes to /1, /usr to /usr1 and so on. Is this some kind rescue attempt by LINUX (Fedora Core 3) or by the SATA disk? What can be done to restore the file system? I can log in but if I start a job it runs for minute or two and then the computer crashes. Reinstalling the systems help until the next crash occurs ... Can someone give a hint? Thanks, Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Tue Feb 7 11:52:02 2006 From: "peter.gedeck]-[novartis.com" To: CCL Subject: CCL: UK QSAR and ChemoInformatics Group Meeting - Agenda/Registration are online Message-Id: <-30809-060207112132-11268-8/WzycO4goSwA5htEffBXA _ server.ccl.net> X-Original-From: peter.gedeck:+:novartis.com Content-type: text/plain; charset=us-ascii Date: Tue, 7 Feb 2006 15:21:18 +0000 MIME-Version: 1.0 Sent to CCL by: peter.gedeck|,|novartis.com Dear all, Three years after having hosted a Meeting of the UK QSAR and ChemoInformatics Group, Accelrys is pleased to welcome the Spring 2006 edition of the UK QSAR and ChemoInformatics Group meeting in its Cambridge facilities. Eight key speakers from the pharmaceutical industry and academic research community will be presenting at this meeting. The detailed agenda, abstracts of the presentations, information about lodging in Cambridge, and registration form can be found under: http://www.accelrys.com/events/conferences/2006_april_QSAR_society/index.html As part of this meeting we will have a poster session (over lunch time), as well as a poster competition. Scientists interested in participating to this competition can submit their poster before April 21st 2006. On the afternoon of April 27, Accelrys will run a three hour workshop on physical-based scoring methods (CHARMm). You are also cordially invited to participate to this seminar. Hope to see you all in Cambridge. Dr. Remy Hoffmann Accelrys SARL From owner-chemistry@ccl.net Tue Feb 7 12:44:00 2006 From: "John Hearns john.hearns\a/streamline-computing.com" To: CCL Subject: CCL: LINUX system problem Message-Id: <-30810-060207121602-9009-YgfEKNPo0jZ3uYs1mReWDw_-_server.ccl.net> X-Original-From: John Hearns Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Tue, 07 Feb 2006 17:15:01 +0000 Mime-Version: 1.0 Sent to CCL by: John Hearns [john.hearns#%#streamline-computing.com] On Tue, 2006-02-07 at 11:19 -0500, Ulrike Salzner salzner-x-fen.bilkent.edu.tr wrote: > Sent to CCL by: Ulrike Salzner [salzner:+:fen.bilkent.edu.tr] > Dear all, > we have one PC that is a real lemon. e2label will either display the filesystem label or set it. eg. e2label /dev/hda1 / will set the label on partition hda1 Is your problem machine being re-installed automatically every time using a Kickstart? That will re-label the partitions. But it should not matter if the /etc/fstab is also being updated. So if you manually use e2label, remember to edit the fstab, and your boot loader config if you have root=LABEL=/1 BTW, if a machine is a lemon you should run memtest on it. From owner-chemistry@ccl.net Tue Feb 7 14:06:00 2006 From: "Steve Gwaltney drg51|*|ra.msstate.edu" To: CCL Subject: CCL: ACES Message-Id: <-30811-060207134303-16122-Go2tmmv4z0ex0XKpXuupvA-$-server.ccl.net> X-Original-From: Steve Gwaltney Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 07 Feb 2006 10:56:32 -0600 MIME-Version: 1.0 Sent to CCL by: Steve Gwaltney [drg51::ra.msstate.edu] Crawford, Daniel crawdad]![vt.edu wrote: > Use the "DROP_MO" keyword to freeze core orbitals. For example, if you > want to freeze the lowest three orbitals (ordered by energy), you would > set: DROP_MO=1>3 > > -Daniel This depends on how old your version of ACES2 is. They changed the syntax to "DROPMO=1-3". To know which one to use, either check the manual for your version, or run an example and very carefully check the output. Steve -- Dr. Steven Gwaltney Phone: 662-325-7602 Assistant Professor Fax: 662-325-1618 Department of Chemistry, Mail: Box 9573 Center for Environmental Health Sciences, Mississippi State University and Center for Computational Sciences Mississippi State, MS 39762 From owner-chemistry@ccl.net Tue Feb 7 14:41:01 2006 From: "nokophala##aim.com" To: CCL Subject: CCL: Aquous electrochemistry Message-Id: <-30812-060207095939-26383-uafE97op/TVUn4U1s3BiuA[A]server.ccl.net> X-Original-From: nokophala:aim.com Content-Type: multipart/alternative; boundary="--------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com" Date: Tue, 07 Feb 2006 09:23:39 -0500 MIME-Version: 1.0 Sent to CCL by: nokophala-$-aim.com ----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com Content-Type: text/plain; charset="us-ascii" Thanks for responses so far, everyone. From my current calcs it does seem that one must have the correct structure of the first shell, especially for cationic ions. For H+ is is almost mandatory, but already a single water molecules brings the solvation energy to within an eV of the correct value. Anionic species seem ok'yish even without a shell. Dr Noko Phala E-mail: nokophala]*[aim.com -----Original Message----- > From: Goedele Roos groos[]vub.ac.be To: Phala, Noko Sent: Mon, 6 Feb 2006 14:54:03 -0500 Subject: CCL: Aquous electrochemistry Sent to CCL by: Goedele Roos [groos^-^vub.ac.be] Yes, the first solvatation shell is important, see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997. or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. Struct.: Theochem, 759,(2006), 245. or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, (2005), 71 also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. Chem. 2005, 44, 4024. Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407. Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025. Greetz, Goedele >Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com] >Here's an interesting link: > >http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html > > >Jim > >> -----Original Message----- >> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] >> Sent: Sunday, February 05, 2006 10:22 AM >> To: Kress, Jim >> Subject: CCL: Aquous electrochemistry >> >> Sent to CCL by: nokophala++aim.com >> >> Hi There, >> Is anyone aware of successes in reproducing some of the >> tabulated redox potentials of electrochemical reactions that >> ar elisted i standard electrochemical tables, especiall those >> involving single ions? e.g. Cu >> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the >> selection of appropriate solvation models. I doubt if >> continuum models would require inclusion of at least the >> first shell of water molecules, as these are strongly bound. >> As a starting point I am trying to reproduce the experimental >> value of the 'reference' reaction 2H+ +2e = H2. Even this >> appears tricky. >> >> Thanks in advance, >> >> Noko Phala, Anglo Research >> ______________________________________________________________ >> __________ >> Check Out the new free AIM(R) Mail -- 2 GB of storage and >> industry-leading spam and email virus protection. >> >> >> >> -= This is automatically added to each message by the mailing >> script =- >> To recover the email address of the author of the message, >> please change> Conferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, >> Password: search)> >> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ >> -+-+-+-+-+> > > > Drs. Goedele Roos Dienst Algemene Chemie (ALGC) Vrije Universiteit Brussel (VUB) Pleinlaan 2 B-1050 Brussels Tel: 0032-2-629 35 16 Fax: 0032-2-629 33 17http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection. ----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com Content-Type: text/html; charset="us-ascii"
Thanks for responses so far, everyone. From my current calcs it does seem that one must have the correct structure of the first shell, especially for cationic ions. For H+ is is almost mandatory, but already a single water molecules brings the solvation energy to within an eV of the correct value. Anionic species seem ok'yish even without a shell.  
 



Dr Noko Phala
E-mail: nokophala]*[aim.com
 
 
-----Original Message-----
From: Goedele Roos groos[]vub.ac.be <owner-chemistry]*[ccl.net>
To: Phala, Noko <nokophala]*[aim.com>
Sent: Mon, 6 Feb 2006 14:54:03 -0500
Subject: CCL: Aquous electrochemistry

Sent to CCL by: Goedele Roos [groos^-^vub.ac.be]

Yes, the first solvatation shell is important,
see Uudsemaa, M., Tamm, T., J. Phys. Chem. A 2003, 107, 9997.
or see: M. Namazian, Siahrostami, s., Noorbala, M. R., Coote, m. L., J. Mol. 
Struct.: Theochem, 759,(2006), 245.
or: Shamsipur, M., Alizadeh, Arshadi, S., J. Mol. Struct.: Theochem, 758, 
(2005), 71

also a very good paper Dutton, A., S., Fukuto, J. M., Kendall, N. H., J. Inorg. 
Chem. 2005, 44, 4024.

Baik, M.-H., Friesner, A. J. Phys. Chem. A 2002, 106, 7407.

Patterson, E, Cramer, C., Truhlar, D, JACS, 123 (2001) 2025.


Greetz, Goedele

>Sent to CCL by: "Jim Kress" [ccl_nospam#kressworks.com]
>Here's an interesting link:
>
>http://comp.chem.umn.edu/netstep/2000/february/9truhcram.html
>
>
>Jim 
>
>> -----Original Message-----
>> From: nokophala. ~ .aim.com [mailto:owner-chemistry ~ ccl.net] 
>> Sent: Sunday, February 05, 2006 10:22 AM
>> To: Kress, Jim 
>> Subject: CCL: Aquous electrochemistry
>> 
>> Sent to CCL by: nokophala++aim.com
>> 
>> Hi There,
>> Is anyone aware of successes in reproducing some of the 
>> tabulated redox potentials of electrochemical reactions that 
>> ar elisted i standard electrochemical tables, especiall those 
>> involving single ions? e.g. Cu 
>> --> Cu2+(aq) + 2e-. The key issue that I need coment on here is the
>> selection of appropriate solvation models. I doubt if 
>> continuum models would require inclusion of at least the 
>> first shell of water molecules, as these are strongly bound. 
>> As a starting point I am trying to reproduce the experimental 
>> value of the 'reference' reaction 2H+ +2e = H2. Even this 
>> appears tricky.
>> 
>> Thanks in advance,
>> 
>> Noko Phala, Anglo Research
>> ______________________________________________________________
>> __________
>> Check Out the new free AIM(R) Mail -- 2 GB of storage and 
>> industry-leading spam and email virus protection.
>> 
>> 
>> 
>> -= This is automatically added to each message by the mailing 
>> script =-
>> To recover the email address of the author of the message, 
>> please change> Conferences: 
>> http://server.ccl.net/chemistry/announcements/conferences/
>> 
>> Search Messages: http://www.ccl.net/htdig  (login: ccl, 
>> Password: search)> 
>> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
>> -+-+-+-+-+>
>
>
>

Drs. Goedele Roos
Dienst Algemene Chemie (ALGC)
Vrije Universiteit Brussel (VUB)
Pleinlaan 2
B-1050 Brussels
Tel: 0032-2-629 35 16
Fax: 0032-2-629 33 17E-mail to subscribers: CHEMISTRY]*[ccl.net or use:
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----------MailBlocks_8C7FA093983A4F3_1630_19F3_FWM-D25.sysops.aol.com-- From owner-chemistry@ccl.net Tue Feb 7 16:43:00 2006 From: "Daan van Aalten vdava{:}davapc1.bioch.dundee.ac.uk" To: CCL Subject: CCL: Is there any tool for converting ligand structures in AutoDock format? Message-Id: <-30813-060207163340-12575-ONy0kkO/oLyKBxBsU+uX9A]~[server.ccl.net> X-Original-From: Daan van Aalten Content-Transfer-Encoding: 8bit Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Date: Tue, 7 Feb 2006 20:41:51 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Daan van Aalten [vdava/./davapc1.bioch.dundee.ac.uk] ..alternatively you could use PRODRG - which generates coordinates from the SDfiles, protonates and charges them and writes out PDBQ files directly for input into Autodock (and many other modelling/refinement programs). PRODRG is available as a server at http://davapc1.bioch.dundee.ac.uk/prodrg and a local copy can be requested for free (see FAQ on the website) cheers Daan On Tue, 7 Feb 2006, Gilles Marcou gilles.marcou,+,pharma.u-strasbg.fr wrote: > Sent to CCL by: Gilles Marcou [gilles.marcou!A!pharma.u-strasbg.fr] > Hi, > > I'm not sure if this is what you're searching for... First of all, you should > begin with a 3D model of the ligand, with no ambiguities on ionization state > and tautomer state. It should be easier to use mol2 format. You should care a > lot about atom typing too. > > In the following I assume you are working on an UNIX/Linux workstation or you > have cygwin -or equivalent- installed on your Window$. > > Then you can use the programs distributed with autodock like deftors. They are > interactive but you can answer automatically to the questions using standard > shell syntaxe. For example if you have a seperate mol2 for each of your > ligand in a specific directory, following the Get Started part of the > autodock manual, a bash script would look like: > > for lig in MyLigandsDir/*.mol2; do > $AUTODOCK_DIR/share/deftors $lig < 1 > c > c > EOF > $AUTODOCK_DIR/share/mkdpf3 ${lig/.mol2/.pdbq} protein.pdbqs; > $AUTODOCK_DIR/bin/autodock3 -p ${lig%\.mol2}.protein.dpf -l > ${lig%\.mol2}.protein.dlg; > > In this example for each mol2 file in the directory MyLigandsDir: > > 1/ deftor take the fist cycle proposed as root, select no other root and keep > all proposed dihedral angle for rotamers generation and generates the pdbq. > > 2/ the docking parameter file (.dpf) file is generated using the mol2 file and > the pdbqs of the protein > > 3/ the docking is done according to the instructions of the dpf file. > > Of course this is only an example and you should write a script that fits your > specific needs and you particular molecular library. > > The tools distributed with autodock, while not very efficients are convenient > enough, I think, to treat medium sized libraries. Nonetheless, even if I like > very much autodock, this not really a high throughput docking program. > > Good luck. > > Le Mardi 7 Février 2006 12:49, D.BIO- Gerard Pujadas gerard.pujadas{:}urv.net > a écrit : > > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas^urv.net] > > > > Dear members of the CCL list, > > > > I wonder if there is any tool that can be used to > > transform a set of ligand structures (for > > example, downloaded from the ZINC database) into > > the format required for its use by AutoDock. > > > > With many thanks in advances for your help > > > > Yours sincerely, > > > > Gerard > > -- > Gilles Marcou > Université Louis Pasteur de Strasbourg > Faculté de Pharmacie > Laboratoire de Pharmacochimie de la > Communication Cellulaire, UMR7081 > 74, Route du Rhin, BP24 > 67401 Illkirch > tel.:(0033)(0)3.90.24.42.21 > eMail: marcou=pharma.u-strasbg.fr> > > ############################################################################## Dr. Daan van Aalten Wellcome Trust Senior Fellow / Reader Wellcome Trust Biocentre, Dow Street TEL: ++ 44 1382 344979 Div. of Biol.Chem. & Mol.Microbiology FAX: ++ 44 1382 345764 School of Life Sciences E-mail: see WWW page Univ. of Dundee, Dundee DD1 5EH, UK WWW: http://davapc1.bioch.dundee.ac.uk From owner-chemistry@ccl.net Tue Feb 7 17:18:00 2006 From: "Michael Schmuker schmuker*chemie.uni-frankfurt.de" To: CCL Subject: CCL: LINUX system problem Message-Id: <-30814-060207142054-32361-5tHrVfTFXE04V4vaWBcYyQ\a/server.ccl.net> X-Original-From: Michael Schmuker Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Tue, 7 Feb 2006 19:20:52 +0100 MIME-Version: 1.0 Sent to CCL by: Michael Schmuker [schmuker{}chemie.uni-frankfurt.de] Dear Ulrike, this smells like defective RAM. You can test it with e.g. memtest86 ( http://www.memtest86.com/ ). You can also use a Knoppix CD if you have one laying around; just type "memtest" on the boot screen. The fans are also worth checking; Sometimes they fail, sometimes they get blocked by something. HTH, Michael On Tuesday 07 February 2006 17:21, Ulrike Salzner salzner-x-fen.bilkent.edu.tr wrote: > Sent to CCL by: Ulrike Salzner [salzner:+:fen.bilkent.edu.tr] > Dear all, > we have one PC that is a real lemon. It made problems after about 7 > months of usage and crashes very often. One thing that happens is > that after crashing, all the file systems have changed their lables > by adding a 1. For instance / goes to /1, /usr to /usr1 and so on. > Is this some kind rescue attempt by LINUX (Fedora Core 3) or by the > SATA disk? What can be done to restore the file system? I can log > in but if I start a job it runs for minute or two and then the > computer crashes. Reinstalling the systems help until the next > crash occurs ... Can someone give a hint? > > Thanks, > Ulrike -- Michael Schmuker University of Frankfurt Beilstein Endowed Chair of Cheminformatics http://www.modlab.de From owner-chemistry@ccl.net Tue Feb 7 17:53:00 2006 From: "Samuel Flores samuel.flores=yale.edu" To: CCL Subject: CCL: tinker dynamic error Message-Id: <-30815-060207165601-19781-3Nj2zZwvCfCCfgRczsR8PQ-,-server.ccl.net> X-Original-From: "Samuel Flores" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Feb 2006 16:54:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Samuel Flores" [samuel.flores_-_yale.edu] Hi guys, I am having a puzzling error that perhaps someone could help me with. I am trying to run dynamics on ribosome recycling factor (1DD5) but got an 'Undefined parameters' error. I figured out that the first residue with this problem is PRO 48. There is another praline, PRO 34, which has not missing parameters. I put the two prolines in a file by themselves and ran dynamics, getting the following results: ############################################################################ ## Undefined Torsional Parameters : Type Atom Names Atom Classes Torsion 24-C 17-N 18-C 19-C 1 8 1 3 MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation Does anyone know what's going on? The structure is the following: 31 1 N+ -8.391000 -8.592000 -6.365000 9 2 5 6 10 2 C -8.247000 -9.923000 -6.944000 1 1 3 7 8 3 C -7.252000 -9.922000 -8.190000 2 2 4 17 4 O -6.874000 -11.073000 -8.491000 13 3 5 H -7.822047 -7.936383 -6.881294 19 1 6 H -8.092014 -8.609782 -5.400432 19 1 7 H -7.883000 -10.622000 -6.200000 17 2 8 C -9.667000 -10.332000 -7.472000 1 2 9 11 12 9 C -10.555000 -9.249000 -6.937000 1 8 10 13 14 10 C -9.714000 -8.045000 -6.681000 1 1 9 15 16 11 H -10.252000 -10.774000 -6.634000 17 8 12 H -9.621000 -11.064000 -8.304000 17 8 13 H -11.614000 -9.562000 -6.850000 17 9 14 H -10.486000 -8.356000 -7.600000 17 9 15 H -9.371000 -8.038000 -5.621000 17 10 16 H -10.293000 -7.120000 -6.909000 17 10 17 N 1.436000 -26.521000 -11.070000 8 3 18 24 18 C 1.365000 -25.097000 -10.838000 1 17 19 21 22 19 C -0.032000 -24.715000 -10.380000 3 18 20 31 20 O- -0.825000 -24.563000 -11.291000 14 19 21 H 2.082000 -24.783000 -10.089000 17 18 22 C 1.942000 -24.493000 -12.189000 1 18 23 25 26 23 C 2.801000 -25.661000 -12.756000 1 22 24 27 28 24 C 1.982000 -26.891000 -12.399000 1 17 23 29 30 25 H 3.053000 -24.458000 -12.125000 17 22 26 H 1.562000 -23.472000 -12.400000 17 22 27 H 3.591000 -25.318000 -13.452000 17 23 28 H 2.135000 -26.385000 -13.279000 17 23 29 H 2.326000 -27.310000 -11.426000 17 24 30 H 2.073000 -27.656000 -13.205000 17 24 31 O- -0.143676 -24.252951 -9.223912 14 19 Many thanks, Sam From owner-chemistry@ccl.net Tue Feb 7 18:28:00 2006 From: "Samuel Flores samuel.flores- -yale.edu" To: CCL Subject: CCL: tinker dynamic error Message-Id: <-30816-060207171900-762-NeQIb8d8KiOmVWamoCgNHw]-[server.ccl.net> X-Original-From: "Samuel Flores" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 7 Feb 2006 17:17:48 -0500 MIME-Version: 1.0 Sent to CCL by: "Samuel Flores" [samuel.flores]![yale.edu] Looks like the connectivities are wrong, at least for the two nitrogens. But can anyone tell me why? Sam Samuel Flores Graduate Student Gerstein Lab Office: Bass 437 266 Whitney Avenue New Haven, CT 06520 203.432.5405 Home: 28 Pearl Street New Haven, CT 06511 cell: 203.747.2682 -----Original Message----- > From: Samuel Flores [mailto:samuel.flores:-:yale.edu] Sent: Tuesday, February 07, 2006 4:55 PM To: 'CCL Subscribers' Subject: tinker dynamic error Hi guys, I am having a puzzling error that perhaps someone could help me with. I am trying to run dynamics on ribosome recycling factor (1DD5) but got an 'Undefined parameters' error. I figured out that the first residue with this problem is PRO 48. There is another praline, PRO 34, which has not missing parameters. I put the two prolines in a file by themselves and ran dynamics, getting the following results: ############################################################################ ## Undefined Torsional Parameters : Type Atom Names Atom Classes Torsion 24-C 17-N 18-C 19-C 1 8 1 3 MECHANIC -- Some Required Potential Energy Parameters are Undefined TINKER is Unable to Continue; Terminating the Current Calculation Does anyone know what's going on? The structure is the following: 31 1 N+ -8.391000 -8.592000 -6.365000 9 2 5 6 10 2 C -8.247000 -9.923000 -6.944000 1 1 3 7 8 3 C -7.252000 -9.922000 -8.190000 2 2 4 17 4 O -6.874000 -11.073000 -8.491000 13 3 5 H -7.822047 -7.936383 -6.881294 19 1 6 H -8.092014 -8.609782 -5.400432 19 1 7 H -7.883000 -10.622000 -6.200000 17 2 8 C -9.667000 -10.332000 -7.472000 1 2 9 11 12 9 C -10.555000 -9.249000 -6.937000 1 8 10 13 14 10 C -9.714000 -8.045000 -6.681000 1 1 9 15 16 11 H -10.252000 -10.774000 -6.634000 17 8 12 H -9.621000 -11.064000 -8.304000 17 8 13 H -11.614000 -9.562000 -6.850000 17 9 14 H -10.486000 -8.356000 -7.600000 17 9 15 H -9.371000 -8.038000 -5.621000 17 10 16 H -10.293000 -7.120000 -6.909000 17 10 17 N 1.436000 -26.521000 -11.070000 8 3 18 24 18 C 1.365000 -25.097000 -10.838000 1 17 19 21 22 19 C -0.032000 -24.715000 -10.380000 3 18 20 31 20 O- -0.825000 -24.563000 -11.291000 14 19 21 H 2.082000 -24.783000 -10.089000 17 18 22 C 1.942000 -24.493000 -12.189000 1 18 23 25 26 23 C 2.801000 -25.661000 -12.756000 1 22 24 27 28 24 C 1.982000 -26.891000 -12.399000 1 17 23 29 30 25 H 3.053000 -24.458000 -12.125000 17 22 26 H 1.562000 -23.472000 -12.400000 17 22 27 H 3.591000 -25.318000 -13.452000 17 23 28 H 2.135000 -26.385000 -13.279000 17 23 29 H 2.326000 -27.310000 -11.426000 17 24 30 H 2.073000 -27.656000 -13.205000 17 24 31 O- -0.143676 -24.252951 -9.223912 14 19 Many thanks, Sam From owner-chemistry@ccl.net Tue Feb 7 22:29:01 2006 From: "Raji Raji raji(_)anal.chem.tohoku.ac.jp" To: CCL Subject: CCL: How to run AutoDock Message-Id: <-30817-060207222724-17635-fbHvn1kyfXel/BuO7rteQg**server.ccl.net> X-Original-From: "Raji Raji" Sent to CCL by: "Raji Raji" [raji%a%anal.chem.tohoku.ac.jp] Dear CCL Subscribers, Can any one tell me how to run AutoDock after unzipp the files? How to set up the path and what command I have to use to execute AutoDock? Even I dont know AutoDock is having GUI mode or only CLI mode. How do create the protein/DNA/Ligand structures for AutoDock, I have to use some other visualization (like gausview, cerius, maestro) software? Is it possible to do all the calculations (receptor grid making, and docking) using GUI? Looking forward for your reply. Thanks in advance. Sincerely, Raji.