From chemistry-request@server.ccl.net Mon Feb 12 04:42:43 2001 Received: from gate.pliva.hr (gate.pliva.hr [195.29.208.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1C9gew12179 for ; Mon, 12 Feb 2001 04:42:41 -0500 Received: by gate.pliva.hr; (8.8.8/1.3/10May95) id KAA06280; Mon, 12 Feb 2001 10:44:55 +0100 (MET) Received: from somewhere by smtpxd Received: from somewhere by smtpxd Sender: sanja@pliva.hr Message-ID: <3A87AF18.D21D9BEE@pliva.hr> Date: Mon, 12 Feb 2001 10:38:32 +0100 From: Sanja Sekusak X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.18 i686) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: jaguar Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everybody, recently I started using Jaguar program from Schroedinger Inc. For some of the systems I obtained error messages like: t p i c r RMS maximum e d i u i energy density DIIS r t s t d total energy change change error etot 1 N N 2 U -2481.51723473844 3.2E-01 2.6E-01 etot 2 Y Y 6 M -2486.10562276824 4.6E+00 1.0E-02 1.5E-01 ERROR: fatal error -- see standard output etot 3 N N 2 U -2699.88618055683 2.1E+02 1.0E-02 1.5E-01 Error: jaguar died in program scf Sometimes this problem can be solved using a fine grid for the dft calculation, but in some cases I couldnt get around it. Any suggestions are very welcome. Best regards, Sanja Sekusak From chemistry-request@server.ccl.net Mon Feb 12 04:42:46 2001 Received: from rudjer.irb.hr (sekusak@rudjer.irb.hr [161.53.128.19]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1C9giw12186 for ; Mon, 12 Feb 2001 04:42:45 -0500 Received: from localhost (sekusak@localhost) by rudjer.irb.hr (8.10.0/8.10.0VS) with ESMTP id f1C9gfc22280 for ; Mon, 12 Feb 2001 10:42:41 +0100 (MET) Date: Mon, 12 Feb 2001 10:42:39 +0100 (MET) From: Sanja Sekusak To: CHEMISTRY@ccl.net Subject: jaguar Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, recently I started using Jaguar program from Schroedinger Inc. For some systems I obtained error messages like: t p i c r RMS maximum e d i u i energy density DIIS r t s t d total energy change change error etot 1 N N 2 U -2481.51723473844 3.2E-01 2.6E-01 etot 2 Y Y 6 M -2486.10562276824 4.6E+00 1.0E-02 1.5E-01 ERROR: fatal error -- see standard output etot 3 N N 2 U -2699.88618055683 2.1E+02 1.0E-02 1.5E-01 Error: jaguar died in program scf Sometimes this problem can be solved using a fine grid for the dft calculation, but in some cases I couldnt get around it. Any suggestions are very welcome. Best regards, Sanja Sekusak From chemistry-request@server.ccl.net Mon Feb 12 12:00:49 2001 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CH0mw14767 for ; Mon, 12 Feb 2001 12:00:48 -0500 Received: from erica.schrodinger.com (erica.schrodinger.com [192.156.98.3]) by schrodinger.com (8.8.5/8.8.5) with SMTP id JAA16220; Mon, 12 Feb 2001 09:00:34 -0800 Date: Mon, 12 Feb 2001 09:00:33 -0800 (PST) From: Schrodinger Technical Support To: chemistry@ccl.net cc: help@schrodinger.com Subject: CCL:Jaguar SCF problem In-Reply-To: <3A87FA99.531FB67E@anterio.com> Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY=------------EF61DAA11434FF3C7F36829F Content-Transfer-Encoding: QUOTED-PRINTABLE Content-ID: This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. --------------EF61DAA11434FF3C7F36829F Content-Type: TEXT/PLAIN; CHARSET=iso-8859-1 Content-ID: Hello Sanja, The best way to deal with this kind of SCF convergence problem is to include the "iacscf=1" keyword setting in the &gen section of your input file. This keyword was especially developed to handle troublesome SCF convergence. It automatically increases the accuracy and also employs a variable vshift to stabilize the SCF. This keyword is documented in Table 8.6.22 of the Jaguar manual. Sincerely, Dale Braden ---------------------------------------------------------------------- Schrodinger Technical Support | http://www.schrodinger.com help@schrodinger.com | 503-299-1150 | 503-299-4532 (fax) Schrodinger, Inc. | 1500 SW First Ave. Suite 1180, Portland OR 97201 ---------------------------------------------------------------------- Date: Mon, 12 Feb 2001 10:38:32 +0100 From: Sanja Sekusak To: CHEMISTRY@ccl.net Subject: CCL:jaguar Hi everybody, recently I started using Jaguar program from Schroedinger Inc. For some of the systems I obtained error messages like: t p i c r RMS maximum e d i u i energy density DIIS r t s t d total energy change change error etot 1 N N 2 U -2481.51723473844 3.2E-01 2.6E-01 etot 2 Y Y 6 M -2486.10562276824 4.6E+00 1.0E-02 1.5E-01 ERROR: fatal error -- see standard output etot 3 N N 2 U -2699.88618055683 2.1E+02 1.0E-02 1.5E-01 Error: jaguar died in program scf Sometimes this problem can be solved using a fine grid for the dft calculation, but in some cases I couldnt get around it. --------------EF61DAA11434FF3C7F36829F-- From chemistry-request@server.ccl.net Sun Feb 11 18:46:25 2001 Received: from bratislava.telecom.sk (bratislava.telecom.sk [195.146.128.61]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1BNkOw10919 for ; Sun, 11 Feb 2001 18:46:24 -0500 Received: from duron-k-7 (std113-ke.telecom.sk [212.5.223.113]) by bratislava.telecom.sk (8.9.3/8.9.3) with SMTP id AAA24905 for ; Mon, 12 Feb 2001 00:47:50 +0100 (MET) Message-ID: <003401c09484$54ceb240$71df05d4@duron-k-7> From: "Ivan" To: Subject: Second negative frequency Date: Mon, 12 Feb 2001 00:42:42 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.5 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 Dear CCL'ers I am working with programme GAMESS and an present time I am facing some problems with TS.I am simulating H-transfer from NH3 bonded to the rest of molecule to another "free" NH3 forming "free"NH4. In TS there are two imaginary frequencies ( 1. - value about 975, that correspond to H-transfer and 2.- value about 36 ) and can't get rid of this second little negative frequency. Firstly I tried to use keywords PURIFY in $STATPT and $FORCE groups to purify hessian matrix but with no results. Then I tried several approachs to find better TS, but all resulted to the same TS. And IRC calculations in both directions are correct, because according to IRC's this TS connects appropriate minimas on both side of the hill.Finally I wanted to to perform IRC folowing the second negative frequency, but GAMESS did not accept the specified frequency ( in $IRC group ). I would very appreciate any help,advice or trick. Stanislav Ivan student From chemistry-request@server.ccl.net Mon Feb 12 05:22:20 2001 Received: from ciril.fr (arcturus.ciril.fr [193.50.27.66]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CAMJw12378 for ; Mon, 12 Feb 2001 05:22:20 -0500 Received: from marlin (marlin.rmn.uhp-nancy.fr [193.54.42.65]) by ciril.fr (8.11.2/8.11.2/Guy-12-01-2001) with SMTP id f1CAMIQ05332 for ; Mon, 12 Feb 2001 11:22:18 +0100 (MET) Message-Id: <200102121022.f1CAMIQ05332@ciril.fr> X-Sender: owalker@ciril.fr X-Mailer: QUALCOMM Windows Eudora Pro Version 4.0.1 Date: Mon, 12 Feb 2001 11:25:18 +0100 To: chemistry@ccl.net From: Olivier Walker Subject: NMR shielding tensor problem Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f1CAMKw12379 Dear collegues, I'm running some NMR calculations on a medium size molecule (C11H8O2) using Gaussian 98 at the MP2 level and a 6-31G basis set. The obtained results are in very good agreement with experiment (carbon-13 NMR isotropic shift appear between 0 and 220ppm) but when i try to use greater basis set like 6-31G* or 6-31G**, I obtain very strange and crazy results like: 8 C Isotropic = -1360.4106 Anisotropy = 2054.8028 XX= -392.6538 YX= 1144.4672 ZX= -223.1761 XY= 622.5548 YY= -2190.5743 ZY= 23.5427 XZ= -420.8500 YZ= 254.1392 ZZ= -1498.0037 Eigenvalues: -2609.6892 -1481.0005 9.4579 or like: 9 C Isotropic =*********** Anisotropy =*********** XX=*********** YX=*********** ZX=*********** XY=*********** YY=*********** ZY=*********** XZ=*********** YZ=*********** ZZ=*********** Eigenvalues:********************************* Does anybody experience the same problem with MP2 calculations? Olivier. ************************************************************* Olivier WALKER Laboratoire de méthodologie RMN Université de NANCY I Faculté des sciences boulevard des aiguillettes B.P.239-54506 Vandoeuvre les Nancy (FRANCE) ************************************************************* Tel:33.3.83.91.20.18 fax:33.3.83.91.23.67 E-mail:Olivier.Walker@rmn.uhp-nancy.fr ************************************************************* From chemistry-request@server.ccl.net Mon Feb 12 05:31:48 2001 Received: from sina.com ([202.106.187.168]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1CAVkw12453 for ; Mon, 12 Feb 2001 05:31:47 -0500 Received: (qmail 11946 invoked by uid 99); 12 Feb 2001 10:34:04 -0000 Message-ID: <20010212103404.11945.qmail@sina.com> From: lijuer@sina.com To: chemistry@ccl.net Subject: problem in using EGO MD! Date: Mon, 12 Feb 2001 18:34:04 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Hi: is there any one doing molecular dynamic using EGO? I run EGO in HPC calculating a protein and enviroment with atoms 40000 in total. I met some problem in this simulation procedure. if someone has experience and has interests to help me. please mail me! Thanks! Lingling Shen ______________________________________ =================================================================== ÐÂÀËÃâ·Ñµç×ÓÓÊÏä (http://mail.sina.com.cn) ÐÂÀËÁÄÌì´ó½±-MP3ÉÌÎñͨDVDÊÖ»ú×ê½äµÈ×ÅÄú£»²¢ÌṩÁÄÓÑËÙÅä·þÎñ (http://newchat.sina.com.cn/love/) From chemistry-request@server.ccl.net Mon Feb 12 08:38:55 2001 Received: from nic.upatras.gr (nic.upatras.gr [150.140.129.30]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f1CDcnw13805 for ; Mon, 12 Feb 2001 08:38:49 -0500 Received: (qmail 2004 invoked from network); 12 Feb 2001 13:38:31 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 12 Feb 2001 13:38:31 -0000 Received: (qmail 15419 invoked from network); 12 Feb 2001 13:42:07 -0000 Received: from milon.physics.upatras.gr (HELO milon) (150.140.158.11) by pythagoras.physics.upatras.gr with SMTP; 12 Feb 2001 13:42:07 -0000 Message-ID: <002201c094f8$fde7c8c0$0b9e8c96@milon.physics.upatras.gr> From: "Christos Garoufalis" To: Subject: g98 oscillator strengths Date: Mon, 12 Feb 2001 15:37:49 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01C09509.C15FCFE0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.72.3110.1 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3110.3 This is a multi-part message in MIME format. ------=_NextPart_000_001F_01C09509.C15FCFE0 Content-Type: text/plain; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable Dear CCL'ers How reliable are the oscillator strengths derived by a TDDFT calculation with g98? Does anyone has any experience with it? And how = can one force g98 to print them out with more decimal digits? Thanks in advance _________________________ C. S. Garoufalis, Department of Physics,=20 University of Patras, Greece _________________________ ------=_NextPart_000_001F_01C09509.C15FCFE0 Content-Type: text/html; charset="iso-8859-7" Content-Transfer-Encoding: quoted-printable
Dear CCL'ers
How reliable are the oscillator strengths derived by = a=20 TDDFT
calculation with g98? Does anyone has any experience = with it?=20 And how can one force g98 to print them out
with more decimal digits?
 
Thanks in advance
_________________________
C. S.=20 Garoufalis,
Department of Physics,
University of Patras,=20 Greece
_________________________
------=_NextPart_000_001F_01C09509.C15FCFE0-- From chemistry-request@server.ccl.net Mon Feb 12 09:57:49 2001 Received: from lx00.csrsrc.mi.cnr.it (IDENT:root@lx00.csrsrc.mi.cnr.it [155.253.3.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CEvmw14167 for ; Mon, 12 Feb 2001 09:57:48 -0500 Received: from localhost.localdomain (IDENT:uucp@localhost.localdomain [127.0.0.1]) by lx00.csrsrc.mi.cnr.it (8.9.3/8.8.7) with ESMTP id PAA09875 for ; Mon, 12 Feb 2001 15:57:47 +0100 Received: from csrsrc.mi.cnr.it (pitpc7.csrsrc.mi.cnr.it [155.253.3.246]) by lx00.csrsrc.mi.cnr.it (AvMailGate-6.6.0.0) id 9871-6AFEE8E8; Mon, 12 Feb 2001 15:57:46 +0100 Sender: alex@csrsrc.mi.cnr.it Message-ID: <3A87F0FD.9AFFA255@csrsrc.mi.cnr.it> Date: Mon, 12 Feb 2001 15:19:41 +0100 From: Alessandro X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i586) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Evaluating alignment of protein sequence Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-AntiVirus: OK (checked by AntiVir Version 6.6.0.0) Dear CCLers, Maybe a bit OT... I have a multisequence alignment of the same protein coming from different species. One of this sequence has quite interesting mutations I'd like to evaluate with a quantitative tool. Does anyone know a good free software that can generate a similarity matrix from the profile? I'll use the matrix to quantitative evaluate the local differencies on the "less similar" sequence to investigate putative key residues. I need something quite realible. Thanks a lot. I'll summarize the answers. Bye, Ale. From chemistry-request@server.ccl.net Mon Feb 12 13:52:55 2001 Received: from mailx.chem.wisc.edu (mailx.chem.wisc.edu [128.104.68.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CIqtw15474 for ; Mon, 12 Feb 2001 13:52:55 -0500 Received: from chem.wisc.edu (bert.chem.wisc.edu [128.104.70.10]) by mailx.chem.wisc.edu (8.9.3/8.9.3) with SMTP id MAA18382 for ; Mon, 12 Feb 2001 12:52:15 -0600 Received: from fozzie by chem.wisc.edu; Mon, 12 Feb 01 12:50 CST Received: from localhost (uddin@localhost) by chem.wisc.edu (8.8.7/8.8.5) with SMTP id MAA06846 for ; Mon, 12 Feb 2001 12:50:25 -0600 Message-Id: Date: Mon, 12 Feb 2001 12:50:25 -0600 (EST) From: Jamal Uddin Subject: Not enough e- to doubly occupy core To: CHEMISTRY@ccl.net In-Reply-To: <3A87AF18.D21D9BEE@pliva.hr> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, In optimizations of cationic transition metal complexes using JAGUAR I get the following error message: start of program hfig initial wavefunction generated automatically from atomic wavefunctions ERROR: fatal error -- debug information follows diasort: Not enough e- to doubly occupy core For transition metal, there is an effective core potential which I used for the calculation of neutral molecules too but there were no error message. I would appreciate any suggestion or help. Thanks, Jamal Uddin UW-Madison From chemistry-request@server.ccl.net Mon Feb 12 15:05:43 2001 Received: from sunflare.ccs.yorku.ca (sunflare.ccs.yorku.ca [130.63.236.128]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CK5fw15834 for ; Mon, 12 Feb 2001 15:05:41 -0500 Received: from sunlight.ccs.yorku.ca (sunlight.ccs.yorku.ca [130.63.236.85]) by sunflare.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id PAA00264; Mon, 12 Feb 2001 15:05:38 -0500 (EST) Received: from localhost (serge@localhost) by sunlight.ccs.yorku.ca (8.9.3/8.9.3) with ESMTP id PAA24490; Mon, 12 Feb 2001 15:05:37 -0500 (EST) X-Authentication-Warning: sunlight.ccs.yorku.ca: serge owned process doing -bs Date: Mon, 12 Feb 2001 15:05:36 -0500 (EST) From: "S.I.Gorelsky" X-X-Sender: To: Christos Garoufalis cc: Subject: Re: CCL:g98 oscillator strengths In-Reply-To: <002201c094f8$fde7c8c0$0b9e8c96@milon.physics.upatras.gr> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Dear CCL'ers > How reliable are the oscillator strengths derived by a TDDFT > calculation with g98? Does anyone has any experience with it? And how can one force g98 to print them out > with more decimal digits? > > Thanks in advance > _________________________ > C. S. Garoufalis, > Department of Physics, > University of Patras, Greece > _________________________ > Dear Christos. I run TDDFT calculations on transition metal systems and find that the oscillator strengths derived by TDDFT are rather accurate (better than ZINDO, for instance, which tend to overestimate intensities of strong transitions by a factor of 2-4). About decimal digits... you do not need very many for oscillator strengths. Two significant figures are just enough. If the number is 0.0001 or smaller, most likely you will not this transition in the electronic spectrum - it is too weak and will be masked by stronger transitions in the spectrum. Regards, ________________________________________________________________ Sergey I. Gorelsky, M. Sc. Department of Chemistry, York University 4700 Keele Street, Toronto, Ontario M3J 1P3 phone (416) 736-2100 ext#77720 and ext#70131 fax: (416) 736-5936 http://www.chem.yorku.ca/grad/SG/ ________________________________________________________________ From chemistry-request@server.ccl.net Mon Feb 12 16:47:16 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CLlGw16482 for ; Mon, 12 Feb 2001 16:47:16 -0500 Received: from mail.chem.tamu.edu ([165.91.179.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Mon, 12 Feb 2001 15:58:43 -0600 Message-ID: <3A8859BE.9809433D@mail.chem.tamu.edu> Date: Mon, 12 Feb 2001 15:46:38 -0600 From: lakshmi@mail.chem.tamu.edu (Sahasranaman Mahalakshmi) X-Mailer: Mozilla 4.05 [en] (WinNT; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: MOLCAS users Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear cclers, I would like to know if there are any users of RASSCF program of MOLCAS package. I would like to know how to use the "cleanup" and "SUPSYM" option in RASSCF. I am working with a linear molecule. I have gone through the on-line manual of MOLCAS with example of NiH. I would like to know how to set up the input with "cleanup" and "SUPSYM" option as its not very clear to me. Thank you very much for this help. Thanking You, Mahalakshmi E-mail : lakshmi@mail.chem.tamu.edu From chemistry-request@server.ccl.net Mon Feb 12 17:49:05 2001 Received: from mallard.duc.auburn.edu (mallard2.duc.auburn.edu [131.204.2.23]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CMn5w16774 for ; Mon, 12 Feb 2001 17:49:05 -0500 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.8.8+Sun/8.7.2) with SMTP id QAA16346 for ; Mon, 12 Feb 2001 16:49:06 -0600 (CST) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Mon, 12 Feb 2001 16:49:06 -0600 (CST) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: about value Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers; Maybe Simple question, from Gaussian result, there are two values in output like; S**2 before annihilation 0.7592, after 0.7501 Which value Do I have yo report in article? Any help would be appreciated. Best regards, Tommy Kwon Department of Chemistry Auburn University Auburn, AL 36849 From chemistry-request@server.ccl.net Mon Feb 12 20:36:53 2001 Received: from M2W045.MAIL2WEB.COM (M2W045.mail2web.com [168.144.108.45]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1D1arw17207 for ; Mon, 12 Feb 2001 20:36:53 -0500 Received: from m2w045 [168.144.108.45] by M2W045.MAIL2WEB.COM with ESMTP (SMTPD32-6.05) id AF9925940052; Mon, 12 Feb 2001 20:36:25 -0500 X-Originating-IP: 161.142.100.85 X-URL: http://www.mail2web.com/ Subject: autodock3-atmtobnd Sender: "nepenthes@vplaces.net" From: "nepenthes@vplaces.net" Date: Mon, 12 Feb 2001 20:36:25 -0500 To: "chemistry@ccl.net" Reply-To: rowyna@vplaces.net X-Priority: 3 X-MSMail-Priority: Normal MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Mailer: JMail 3.7.0 by Dimac (www.dimac.net) Message-Id: <200102122036594.SM00904@m2w045> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-Printable to 8bit by server.ccl.net id f1D1arw17208 Hi, I am a new user to Autodock3. There is this conversion from 'bnd' file to 'atm' file using atmtobnd. Since atmtobnd was not compiled for the workstation I am using, SGI Irix 6.5, I tried to run the atmtobnd.c file. It comes up with a error message: neuron 37% atmtobnd.c atmtobnd.c: /AppleKongsi: cannot execute atmtobnd.c: atmtobnd.alpha: cannot execute atmtobnd.c[3]: syntax error at line 3 : `(' unexpected Is there anybody who can let me know what is the problem? I would really appreaciate some feedback or suggestion. Thank you very much. Rowyna ISB University of Malaya -------------------------------------------------------------------- Mail2Web - Check your email from the web at http://www.mail2web.com/ . From chemistry-request@server.ccl.net Mon Feb 12 15:32:42 2001 Received: from mb2i0.ns.pitt.edu (mb2i0.ns.pitt.edu [136.142.186.36]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CKWgw16004 for ; Mon, 12 Feb 2001 15:32:42 -0500 Received: from recife ("port 2746"@[136.142.153.159]) by pitt.edu (PMDF V5.2-32 #41462) with SMTP id <01K010DCXV6800F0YG@mb2i0.ns.pitt.edu> for chemistry@ccl.net; Mon, 12 Feb 2001 15:32:43 EST Date: Mon, 12 Feb 2001 15:30:38 -0500 From: Gustavo Moura Subject: Getting dipole velocity and RxDel from G98 To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Dear CCL readers, I know that this is a trivial question for the people who know the answer, but I could not find the answer myself. I want G98 to calculate and store in the checkpoint file the dipole velocity and RxDel integrals. From there I know that I can use the rwfdump utility to check them. All I need to find out is which IOps I need to use. I couldn't find it myself in the manual. Thank you very much in advance. Sincerely yours, Gustavo Moura gustavo@dumbo.chem.pitt.edu From chemistry-request@server.ccl.net Mon Feb 12 16:45:41 2001 Received: from hotmail.com (f237.law10.hotmail.com [64.4.15.237]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CLjfw16458 for ; Mon, 12 Feb 2001 16:45:41 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Mon, 12 Feb 2001 13:43:42 -0800 Received: from 128.97.139.222 by lw10fd.law10.hotmail.msn.com with HTTP; Mon, 12 Feb 2001 21:43:41 GMT X-Originating-IP: [128.97.139.222] From: "hu eric" To: chemistry@ccl.net Subject: find general protein binding site Date: Mon, 12 Feb 2001 13:43:41 -0800 Mime-Version: 1.0 Content-Type: text/plain; charset=gb2312; format=flowed Message-ID: X-OriginalArrivalTime: 12 Feb 2001 21:43:42.0081 (UTC) FILETIME=[DDF59710:01C0953C] Hi, all I'm studying a protein which can carry a reaction better than aqueous. Now I need to find a general binding mode with the transition state. Since this protein is very big and can bind a series of small molecules, I really hope there's an effective way to detect the favorable binding mode with the transition state, for example, vdw matching or electronic potential surface. Thank for your recommendation! Best regards, -Eric _________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com. From chemistry-request@server.ccl.net Mon Feb 12 18:19:02 2001 Received: from anchor-post-30.mail.demon.net (anchor-post-30.mail.demon.net [194.217.242.88]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f1CNIxw16948 for ; Mon, 12 Feb 2001 18:19:01 -0500 Received: from mooncott.demon.co.uk ([158.152.180.96]) by anchor-post-30.mail.demon.net with smtp (Exim 2.12 #1) id 14SSFH-00088u-0U for chemistry@ccl.net; Mon, 12 Feb 2001 23:18:59 +0000 Message-ID: Date: Mon, 12 Feb 2001 23:14:34 +0000 To: chemistry@ccl.net From: Roger Hull Subject: Summary: Autodock on Microsoft Windows platform References: <0+DzMGAcn2b6EwNq@mooncott.demon.co.uk> In-Reply-To: <0+DzMGAcn2b6EwNq@mooncott.demon.co.uk> MIME-Version: 1.0 X-Mailer: Turnpike Integrated Version 4.02 U I had two replies to my question (below): (1) Yes, I did compile Autodock 3.0.5 for Windows (98) using djgpp, http://www.delorie.com/djgpp/ , almost without (additional) problems. IIRC the only thing that had to be changed was to remove the file lock code. I did this as I wanted to see if a core dump I got was system specific. The scripts in the Autodock package however use a whole range of different shells, which might make their transfer to windows quite cumbersome. Mikael Johansson University of Helsinki Department of Chemistry http://www.chem.helsinki.fi/ -------------------------------------------------------------------- (2) Of course, under Cygwin, but the autodock compilation have some problems with the memory access - however, this problem occurs also under SUSE Linux (but, when compiled under RedHat and run on Susue - no problems). (Author replied directly to me and has not [so far] responded to my request for his agreement for me to include his name here. Cygwin is a freeware UNIX emulation package, see http://cygwin.com.) --------------------------------------------------------------------- I can also report my own experience: (3) I have successfully compiled all of the Autodock 3.0.5 under UWIN (another UNIX emulation package, free for academic use, see http://www.research.att.com/sw/tools/uwin/) and Microsoft Visual c++ v6. I have made only limited tests of the compiled modules, but at least the main components (autogrid3 and autodock3) run successfully under Windows NT v4.0 on an IBM PC clone with the supplied test data 3ptb. I will give more details in a separate message when I have done more testing. UWIN (and I think Cygwin) also provide support for running UNIX shell scripts and UNIX utilities such as awk, so I am hopeful that the Autodock scripts will run under UWIN. If anyone is interested in more details of compiling Autodock for UWIN, please contact me. Regards, Roger Hull rogercc@mooncott.demon.co.uk > >Has anyone tried compiling Autodock for Microsoft Windows (NT, 98, 2000, >etc.) ? (Or do you know of anyone who has ?) I have been looking at >doing so for Autodock version 3 using UWIN (a UNIX emulator for >Windows). >