From chemistry-request@server.ccl.net Wed Jul 10 06:07:20 2002 Received: from novel7.farmacia.unina.it ([143.225.223.184]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6AA7Hp01370 for ; Wed, 10 Jul 2002 06:07:18 -0400 Received: from novel7.farmacia.unina.it (localhost [127.0.0.1]) by novel7.farmacia.unina.it (SGI-8.9.3/8.9.3) with ESMTP id MAA28987 for ; Wed, 10 Jul 2002 12:04:51 +0200 (MDT) Sender: luci@novel7.farmacia.unina.it Message-ID: <3D2C06C3.6D72C43D@novel7.farmacia.unina.it> Date: Wed, 10 Jul 2002 12:04:51 +0200 From: Luciana Marinelli X-Mailer: Mozilla 4.76C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: help Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hi autodock users, I don't have any compiletor (as fortran or C) so I can't compile the executable (autotors, atmtobnd,makelaunch, protonate). I am working on a Silicon Graphics R10000 with the operation system IRIX64_6.5, so, who is so kind to send me the above mentioned executables already compiled? thanks a lot luciana From chemistry-request@server.ccl.net Wed Jul 10 07:38:22 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6ABcMp07177 for ; Wed, 10 Jul 2002 07:38:22 -0400 Received: from csd-dd0oht6l3yg (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6ABcLqX025769 for ; Wed, 10 Jul 2002 08:38:21 -0300 (ADT) Received: FROM pop.unb.ca BY csd-dd0oht6l3yg ; Wed Jul 10 08:37:58 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA24496; Wed, 10 Jul 2002 08:38:21 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Wed, 10 Jul 2002 08:38:27 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List , luci@novel7.farmacia.unina.it X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:problem with mol2topdb script Message-ID: <3D2A5A58@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Luciana, I have had this problem too when I installed Autodock 3.05 on my system (SGI Irix v6.5). The "gawk" error message, you have to edit the "mol2topdbq" script so that it calls "awk" instead of "gawk". This can be done with the text editor vi or jot. As for the files being empty, it doesnt say this in the Autodock manual, but you have to specify an output filename for the files. An example would be: % mol2topdbq 1L5G.mol2 > 1L5G.pdbq I would also recommend using AutodockTools (ADT) to prepare your files for docking, as it is much easier than using the scripts. ADT can be interesting to set up, but I have got it to work on my SGI. Hope this helps, Robert >===== Original Message From Luciana Marinelli ===== >hallo, >I am a new AUTODOCK user, I have problem with mol2topdb script. >I am working on a silicon graphics with an operating system: IRIX64 >Release 6. I have download the new one version of autodock. >I have downloaded my protein from PDB and I have added H and charges by >sybyl as you explain in the user guide, than I saved it as mol2 file, >but when I try to run the script that should convert the mol2 file into >the pdbq I have this output: >% mol2topdbq 1L5G.pdb >gawk - Command not found >% > > >if I try to run directly the mol2topdbq.awk I obtain: >% mol2topdbq.awk 1L5G.mol2 >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk: BEGIN: not >found >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk[2]: >haveAtoms: not found >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk[3]: >haveSubStr: not found >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk[4]: resnum: >not found >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk[5]: >allPossibleChainIDs: not found >/usr/people/antonio/Autodock/dist305/share//mol2topdbq.awk[6]: syntax >error at line 6 : `(' unexpected > >I also tryed to use mol2cnv script and I obtain: > >novel7 83% mol2cnv 1L5G.mol2 > >Converting from Sybyl mol2 format to PDBQ format > >gawk - Command not found >Sorting "1L5G.pdbq" by residue number. > >Removing any lone pairs > >gawk - Command not found >Renumbering atoms after sorting by residue number. > >Checking charges in "1L5G.pdbq", using "chckqs"; >All errors held in "1L5G.err" > >Here are the contents of 1L5G.err > >the 1L5G.err and the 1L5G.pdbq are empity. > >I also try to use as imput file the 3PTB.pdb and I have add the H and >charge by sybyl and save it as .mol2, but I have exactly the same >problems. could you imagin why? anyway, I attached my mol2 file >thank you in advance >luciana ******************************** Robert Flight Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca tel: (506) 461-5760 ******************************** From chemistry-request@server.ccl.net Wed Jul 10 07:42:42 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6ABgfp07301 for ; Wed, 10 Jul 2002 07:42:41 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 17SFnF-0002eq-00; Wed, 10 Jul 2002 11:38:01 +0000 Date: Wed, 10 Jul 2002 11:38:01 +0000 (GMT) From: Szilveszter Juhos To: Luciana Marinelli cc: chemistry@ccl.net Subject: Re: CCL:help In-Reply-To: <3D2C06C3.6D72C43D@novel7.farmacia.unina.it> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Though not Autodock, but still you can find free compilers to download at http://freeware.sgi.com/index-by-alpha.html As I see it is gcc 3.0.4 currently available, still you will need your sysadmin's help to install it. I do not know Autodock's code, if gcc3xx complains for old-style declarations/syntax, you can use the -fpermissive switch. Szilva From chemistry-request@server.ccl.net Wed Jul 10 07:49:25 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6ABnPp07443 for ; Wed, 10 Jul 2002 07:49:25 -0400 Received: from csd-dd0oht6l3yg (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6ABnOqX029077 for ; Wed, 10 Jul 2002 08:49:25 -0300 (ADT) Received: FROM pop.unb.ca BY csd-dd0oht6l3yg ; Wed Jul 10 08:49:01 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id IAA28319; Wed, 10 Jul 2002 08:49:24 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Wed, 10 Jul 2002 08:49:30 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List , Luciana Marinelli X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:help Message-ID: <3D2A5F49@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Luciana, A compiler is a good thing to have, especially if you want to install AutodockTools. You can find one for your system at http://freeware.sgi.com/index-by-alpha.html (download gcc-3.0.4), or at the GCC website http://gcc.gnu.org/. I have installed and used the one available > from the SGI freeware site, it works quite well. Good luck, Robert >===== Original Message From Luciana Marinelli ===== >hi autodock users, >I don't have any compiletor (as fortran or C) so I can't compile the >executable (autotors, atmtobnd,makelaunch, protonate). I am working on a >Silicon Graphics R10000 with the operation system IRIX64_6.5, so, who is >so kind to send me the above mentioned executables already compiled? >thanks a lot >luciana > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net ******************************** Robert Flight Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca tel: (506) 461-5760 ******************************** From chemistry-request@server.ccl.net Wed Jul 10 08:14:01 2002 Received: from netmaster.kds.com.ua ([194.44.106.42]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6ACDxp08274 for ; Wed, 10 Jul 2002 08:14:00 -0400 Received: from akhavr by netmaster.kds.com.ua with local (Exim 3.22 #1) id 17SGLW-000878-00; Wed, 10 Jul 2002 15:13:26 +0300 To: Luciana Marinelli Cc: chemistry@ccl.net Subject: Re: help References: <3D2C06C3.6D72C43D@novel7.farmacia.unina.it> From: Andrey Khavryuchenko Organization: KDS Software Group X-Attribution: AVK Date: 10 Jul 2002 15:13:22 +0300 In-Reply-To: <3D2C06C3.6D72C43D@novel7.farmacia.unina.it> Message-ID: Lines: 16 User-Agent: Gnus/5.0808 (Gnus v5.8.8) XEmacs/21.4 (Academic Rigor) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Luciana, "LM" == Luciana Marinelli wrote: LM> I don't have any compiletor (as fortran or C) so I can't compile the LM> executable (autotors, atmtobnd,makelaunch, protonate). I am working on a LM> Silicon Graphics R10000 with the operation system IRIX64_6.5, so, who is LM> so kind to send me the above mentioned executables already compiled? You may use free compilers from GNU project: gcc and g77. Google tells me that g77 binaries are available from http://gcc.gnu.org/install/binaries.html -- Andrey V Khavryuchenko http://www.kds.com.ua/ Software Solutions From chemistry-request@server.ccl.net Tue Jul 9 19:49:44 2002 Received: from smtp.laposte.net ([213.30.181.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g69Nnhp21254 for ; Tue, 9 Jul 2002 19:49:43 -0400 Received: from nouveaupc (217.128.255.253) by smtp.laposte.net (6.0.053) id 3D2A2BF000014E06 for chemistry@ccl.net; Wed, 10 Jul 2002 01:48:36 +0200 Message-ID: <001601c227a3$1db021f0$3b96fea9@nouveaupc> From: "Alexandre Hocquet" To: Subject: CHELPG and AIM Date: Wed, 10 Jul 2002 01:48:24 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01C227B3.E093FF60" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0013_01C227B3.E093FF60 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable > one-center overlap integrals). Like most such schemes, it is an = arbitrary > scheme for assigning charges (since "atomic charges" are not = unambiguously > defined, at least outside of Bader's AIM theory). I would say, like ALL schemes, be they inside or outside Bader's AIM = theory. Atomic charges are just impossible to define as a physical observable. People may stick the word "rigorous" in front ot their theories if this = make them feel better. Bader's AIM theory is a wonderful and useful tool, the kind that you can extract a lot of chemical insight out of it, but its definition of = charge is only one among the others, with its strengths, weaknesses and = ambiguities. ------------------------------------------------------------ Alexandre HOCQUET Laboratoire de Physicochimie Biomol=E9culaire et Cellulaire UMR CNRS 7033 hocquet@ccr.jussieu.fr Fax: 33 1 44277560 LPBC, case courrier 138 4 Place Jussieu, 75252 PARIS Cedex 05 France ------------------------------------------------------------ ------=_NextPart_000_0013_01C227B3.E093FF60 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
> one-center=20 overlap integrals). Like most such schemes, it is an arbitrary
> = scheme=20 for assigning charges (since "atomic charges" are not = unambiguously
>=20 defined, at least outside of Bader's AIM theory).

I would say, = like ALL=20 schemes, be they inside or outside Bader's AIM theory.
Atomic charges = are=20 just impossible to define as a physical observable.
People may stick = the word=20 "rigorous" in front ot their theories if this make
them feel=20 better.
Bader's AIM theory is a wonderful and useful tool, the kind = that you=20 can
extract a lot of chemical insight out of it, but its definition = of charge=20 is
only one among the others, with its strengths, weaknesses and=20 ambiguities.
---------------------------------------------------------= ---
Alexandre=20 HOCQUET
Laboratoire de Physicochimie Biomol=E9culaire et = Cellulaire
UMR CNRS=20 7033
hocquet@ccr.jussieu.fr
Fax: 33 1 44277560
LPBC, case = courrier 138
4=20 Place Jussieu, 75252 PARIS Cedex 05=20 France
------------------------------------------------------------
------=_NextPart_000_0013_01C227B3.E093FF60-- From chemistry-request@server.ccl.net Tue Jul 9 22:22:35 2002 Received: from hotmail.com ([64.4.21.149]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6A2MZp03319 for ; Tue, 9 Jul 2002 22:22:35 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 9 Jul 2002 19:22:29 -0700 Received: from 203.197.85.118 by lw14fd.law14.hotmail.msn.com with HTTP; Wed, 10 Jul 2002 02:22:28 GMT X-Originating-IP: [203.197.85.118] From: "S. R. Gadre" To: CHEMISTRY@server.ccl.net Cc: gadre@chem.unipune.ernet.in Subject: Ab initio quality electron densities and electrostatic potentials Date: Wed, 10 Jul 2002 02:22:28 +0000 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 10 Jul 2002 02:22:29.0252 (UTC) FILETIME=[A3A15440:01C227B8] Dear Colleagues : This is update of a mail sent about 6 months' ago. WE have developed a program for geeting ab initio quality molecular electron densities, MED (typical error at any point being less than 0.5 per cent) and electrostatic potentials, MESP (typical error at any point being less than 1.5 per cent). The program has been tested for molecules containing about 1000 atoms. The MESP thus generated could be used for studying weak intermolecular interactions with small molecules. Anyone interested in applying it to a chemical/biological problem? ............Shridhar Gadre _________________________________________________________________ Send and receive Hotmail on your mobile device: http://mobile.msn.com From chemistry-request@server.ccl.net Wed Jul 10 04:48:06 2002 Received: from hotmail.com ([64.4.21.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6A8m6p29232 for ; Wed, 10 Jul 2002 04:48:06 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Wed, 10 Jul 2002 01:48:01 -0700 Received: from 141.223.180.14 by lw14fd.law14.hotmail.msn.com with HTTP; Wed, 10 Jul 2002 08:48:00 GMT X-Originating-IP: [141.223.180.14] From: "Yi Hai-Bo" To: chemistry@ccl.net Date: Wed, 10 Jul 2002 16:48:00 +0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 10 Jul 2002 08:48:01.0418 (UTC) FILETIME=[7F79BEA0:01C227EE] Dear Cclers, I¡¯m using TD-DFT method to calculate excitation energy in a supermolecule, D¡­A, which the separate distance is about 0.40 nm. The calculations show an electron transfers from D to A, but the excitation energy is too small, just about 0.81eV, actually should be about 2.2eV. The result: Excited State 1: Singlet-B2 0.8152 eV 1520.85 nm f=0.0000 56 -> 57 0.70710 Total Energy, E(RPA) = -683.363938806 I don¡¯t know why? I appreciate any insight. Thanks! HaiBO Yi _________________________________________________________________ Ãâ·ÑÏÂÔØ MSN Explorer: http://explorer.msn.com/lccn/ From chemistry-request@server.ccl.net Wed Jul 10 10:05:49 2002 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6AE5np13806 for ; Wed, 10 Jul 2002 10:05:49 -0400 Received: (qmail 2809 invoked from network); 10 Jul 2002 14:12:50 -0000 Received: from unknown (HELO test) (212.244.147.4) by mail.fqspl.com.pl with SMTP; 10 Jul 2002 14:12:50 -0000 Message-ID: <009901c2281b$46bb8e40$320a0a0a@test> From: "Victor Anisimov" To: Subject: Accuracy question Date: Wed, 10 Jul 2002 16:05:31 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="koi8-r" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, Based on my short investigation I could learn that HF/6-31G* is the most popular method for electrostatic parameter optimization in Amber, Charmm, OPLS and perhaps in other prominent force fields with the aim of the description of molecular electrostatic potential of protein systems. Here I'd like to ask experts in this field. Is it the correct conclusion I derived or perhaps other quantum-chemistry methods are more popular for the purpose of electrostatic parameters development, e.g. databases of ESP charges of amino acids or similar. Thank you in advance. I will summarise the responses promptly. With best regards, Victor. -- Victor Anisimov FQS Poland, Krakow. From chemistry-request@server.ccl.net Wed Jul 10 11:41:03 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6AFf2p16076 for ; Wed, 10 Jul 2002 11:41:02 -0400 Received: from localhost (fgonzale@localhost) by lauca.usach.cl (8.11.6/8.11.6) with ESMTP id g6AFaUU02165 for ; Wed, 10 Jul 2002 11:36:30 -0400 Date: Wed, 10 Jul 2002 11:36:30 -0400 (CLT) From: Fdo Danilo Gonzalez Nilo To: Subject: StereoView red and blue Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all,... I'm looking for a free software for molecular display in stereo using red and blue method. I will appreciate any information about that (software or another option). Thanks a lot again, Danilo/// ******************************************************************** Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:814 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** From chemistry-request@server.ccl.net Wed Jul 10 12:17:54 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6AGHrp16889 for ; Wed, 10 Jul 2002 12:17:54 -0400 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.36 #3) id 17SK6V-0005V1-04; Wed, 10 Jul 2002 17:14:11 +0100 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id 3K4Q5KWY; Wed, 10 Jul 2002 17:14:35 +0100 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id <3JTK7FFH>; Wed, 10 Jul 2002 17:14:35 +0100 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE1451@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'Fdo Danilo Gonzalez Nilo'" , chemistry@ccl.net Subject: RE: StereoView red and blue Date: Wed, 10 Jul 2002 17:14:34 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean Deep View allows red blue (and other) stereo display: http://www.expasy.ch/spdbv/ Mike -----Original Message----- From: Fdo Danilo Gonzalez Nilo [mailto:fgonzale@lauca.usach.cl] Sent: 10 July 2002 16:37 To: chemistry@ccl.net Subject: CCL:StereoView red and blue Hi all,... I'm looking for a free software for molecular display in stereo using red and blue method. I will appreciate any information about that (software or another option). Thanks a lot again, Danilo/// ******************************************************************** Danilo Gonzalez N. University of Santiago de Chile Faculty of Chemistry and Biology, Computational Chemistry Lab. Casilla 40, Correo 33, Santiago, Chile Fono: (562) 681 1542 Anexo:814 E-mail : fgonzale@lauca.usach.cl Fax : (562) 681 2108 ************************************************************************** -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Wed Jul 10 20:37:43 2002 Received: from mxout4.cac.washington.edu ([140.142.33.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6B0bgp02943 for ; Wed, 10 Jul 2002 20:37:43 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout4.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g6B0bYS4004722 for ; Wed, 10 Jul 2002 17:37:35 -0700 Received: FROM smtp.washington.edu BY mailscan-out1.cac.washington.edu ; Wed Jul 10 17:37:33 2002 -0700 Received: from donald ([128.95.128.116]) by smtp.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g6B0bXTZ030528 for ; Wed, 10 Jul 2002 17:37:33 -0700 Message-ID: <000701c22872$79218d60$74805f80@donald> From: "Carsten Detering" To: Subject: Gasteiger charges and Babel Date: Thu, 11 Jul 2002 02:32:44 +0200 Organization: University of Washington MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Dear CCLers, I wonder how it is possible to assign Gasteiger charges to structures with Babel. I looked on the web site and in the manual, but couldn't find a hint. Would someone be so kind and point out to me how that works?? Thanks a lot in advance, Carsten From chemistry-request@server.ccl.net Wed Jul 10 22:49:32 2002 Received: from ALPHA9.CC.MONASH.EDU.AU ([130.194.1.9]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6B2nVp06595 for ; Wed, 10 Jul 2002 22:49:31 -0400 Received: from kapow.its.monash.edu.au ([130.194.1.71]) by vaxh.cc.monash.edu.au (PMDF V5.2-31 #39306) with ESMTP id <01KJYWGG6CNW8ZNV4K@vaxh.cc.monash.edu.au> for chemistry@ccl.net; Thu, 11 Jul 2002 12:49:26 +1000 Received: from kapow (unknown [127.0.0.1]) by localhost (Postfix) with ESMTP id 37B1020006 for ; Thu, 11 Jul 2002 02:49:26 +0000 (/etc/localtime) Received: from MCHEM217007 (mchem-217-007.vcp.monash.edu.au [130.194.217.7]) by kapow.its.monash.edu.au (Postfix) with SMTP id 2429120006 for ; Thu, 11 Jul 2002 12:49:21 +1000 (EST) Date: Thu, 11 Jul 2002 12:49:21 +1000 From: Jerome Wielens Subject: error with dock4.0.1 To: chemistry@ccl.net Message-id: <007f01c22885$8ed04350$07d9c282@vcp.monash.edu.au> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-Mailer: Microsoft Outlook Express 6.00.2600.0000 Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT X-Priority: 3 X-MSMail-priority: Normal Dear all, I have been using Dock 4.0.1 and am having problems with a few compounds. Dock is breaking apart the starting structure and only docking a portion of the ligand. The error reported in the dock.out file was: WARNING shrink_list: No members provided This error occured when I ran Dock 4.0.1 on either a unix or linux platform. The starting structure was retinoic acid. The same error occured for isoretinoin. These were not the only cases. The starting structures were fine. I also rebuilt these structures to make sure with the same error occuring. I cannot find any information about this error in the Dock manual. Can anyone tell me what this error means and how I can avoid it. Thanks Jerome Wielens