From chemistry-request@server.ccl.net Fri Nov 30 00:52:44 2001 Received: from eyou.com ([61.136.62.74]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAU5qhN06352 for ; Fri, 30 Nov 2001 00:52:43 -0500 Received: (qmail 70517 invoked by alias); 30 Nov 2001 13:52:38 +0800 Received: from unknown (HELO eyou.com) (172.16.2.1) by 172.16.1.2 with SMTP; 30 Nov 2001 13:52:38 +0800 Received: (qmail 65148 invoked by uid 65534); 30 Nov 2001 13:52:39 +0800 Date: 30 Nov 2001 13:52:39 +0800 Message-ID: <20011130135239.65147.qmail@eyou.com> From: "wang jianguo" To: chemistry@ccl.net Reply-To: "wang jianguo" Subject: ask for help hello, Everybody. I have met with some trouble in running the Dock4.0 programms.I used precompiled files, but I always got the error message like this: autoMS epsps.pdb 5 1.4 _______________________________________________________________________ Preparing input for surface calculation... 1850:/usr/people/wjg/dock4.0/bin/pdb2ms: rld: Fatal Error: Cannot Successfully Map soname 'libftn.so' under any of the filenames /usr/lib/libftn.so:/usr/lib/internal/libftn.so:/lib/libftn.so:/lib/cmplrs/cc/l ibftn.so:/usr/lib/cmplrs/cc/libftn.so:/opt/lib/libftn.so:/usr/lib/libftn.so.1: /usr/lib/internal/libftn.so.1:/lib/libftn.so.1:/lib/cmplrs/cc/libftn.so.1:/usr /lib/cmplrs/cc/libftn.so.1:/opt/lib/libftn.so.1: _______________________________________________________________________ Performing QCPE MS calculation... 1954:/usr/people/wjg/dock4.0/bin/qcpe_ms: rld: Fatal Error: Cannot Successfully Map soname 'libftn.so' under any of the filenames /usr/lib/libftn.so:/usr/lib/internal/libftn.so:/lib/libftn.so:/lib/cmplrs/cc/l ibftn.so:/usr/lib/cmplrs/cc/libftn.so:/opt/lib/libftn.so:/usr/lib/libftn.so.1: /usr/lib/internal/libftn.so.1:/lib/libftn.so.1:/lib/cmplrs/cc/libftn.so.1:/usr /lib/cmplrs/cc/libftn.so.1:/opt/lib/libftn.so.1: Cannot open CONTACT: No such file or directory Cannot open REENTRANT: No such file or directory _______________________________________________________________________ Converting output to SPHGEN input format... 1967:/usr/people/wjg/dock4.0/bin/reformatms: rld: Fatal Error: Cannot Successfully Map soname 'libftn.so' under any of the filenames /usr/lib/libftn.so:/usr/lib/internal/libftn.so:/lib/libftn.so:/lib/cmplrs/cc/l ibftn.so:/usr/lib/cmplrs/cc/libftn.so:/opt/lib/libftn.so:/usr/lib/libftn.so.1: /usr/lib/internal/libftn.so.1:/lib/libftn.so.1:/lib/cmplrs/cc/libftn.so.1:/usr /lib/cmplrs/cc/libftn.so.1:/opt/lib/libftn.so.1: ________________________ Almost every executive program encounter such trouble. How to solve the problem? Thank you. Sincerely yours Jianguo Wang Elemento-Organic Chemistry Institute, National Pesticide Engeering Research Center, Nankai University, Tianjin P. R. China voice: 86-22-23503705 fax: 86-22-23505948 e-mail:nkwjg@eyou.com --http://www.eyou.com --稳定可靠的免费电子信箱 语音邮件 移动书签 日历服务 网络存储...亿邮未尽 From chemistry-request@server.ccl.net Fri Nov 30 02:48:21 2001 Received: from sina.com ([202.108.35.251]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAU7mJN10365 for ; Fri, 30 Nov 2001 02:48:20 -0500 Received: (qmail 29596 invoked by uid 99); 30 Nov 2001 07:46:51 -0000 Message-ID: <20011130074651.29595.qmail@sina.com> From: t218gy To: chemistry@ccl.net Subject: About TDDFT MIME-Version: 1.0 Date: Fri, 30 Nov 2001 15:46:51 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear Sir, When I use Guassian98 to deal with open-shell systems, I found that the TDDFT could also do work. But the Guassian's reference say TDDFT could only deal with close-shell systems. I want to know whether the results obtained reliable or not? Thanks in advance. Yi Gao Department of Chemistry Nanjing Univ. P.R.China ______________________________________ =================================================================== 新浪免费电子邮箱 (http://mail.sina.com.cn) 新浪分类信息：轻松订阅，量身定制！周周有礼，大奖等你！ (http://classad.sina.com.cn/) 七种手机图片、千首铃声下载……新浪短信无限精彩! (http://sms.sina.com.cn/) From chemistry-request@server.ccl.net Fri Nov 30 03:03:45 2001 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU83jN10660 for ; Fri, 30 Nov 2001 03:03:45 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se; Fri, 30 Nov 2001 09:03:32 +0100 Received: from werkman.bmc.uu.se (werkman.bmc.uu.se [130.238.37.169]) by XRAY.bmc.uu.se (8.9.3/8.8.7) with ESMTP id JAA06869; Fri, 30 Nov 2001 09:05:15 +0100 Date: Fri, 30 Nov 2001 09:55:54 +0100 (CET) From: David van der Spoel X-X-Sender: To: "mer@chem.wayne.edu" cc: Subject: Re: CCL:dynamical cross-correlation matrices In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 29 Nov 2001, mer@chem.wayne.edu wrote: >Dear All, > I am wondering if anyone knows of any software (preferably free) >that would compute dynamical cross-crrelation matrices for a protein >simulation. What other software could be used to display it in color >coded 2D plot? I have a trajectory in AMBER coordinate file format. gromacs can do it (www.gromacs.org) It can also read AMBER trajectories. the program in the gromacs suite that you want is g_covar, check out the manual at http://www.gromacs.org/documentation/reference_3.0/online/g_covar.html -- Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Nov 30 03:25:43 2001 Received: from bioinfo.ernet.in ([202.41.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU8PgN11233 for ; Fri, 30 Nov 2001 03:25:42 -0500 Received: from localhost (manjari@localhost) by bioinfo.ernet.in (8.8.7/8.8.7) with ESMTP id NAA08435 for ; Fri, 30 Nov 2001 13:57:37 +0530 Date: Fri, 30 Nov 2001 13:57:37 +0530 (IST) From: To: CHEMISTRY@ccl.net Subject: CONTACSYM Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am Sunitha Manjari a JRF at Bioinformatics Centre, Univ of Pune, India. I am interested in a program named CONTACSYM by Sheriff et al which helps in calculating Hydrogen bonds, van der Waal's distances and salt bridges. I tried searching for it on the net but could not get any information. Please send the site from where this program can be obtained or any information in this regard. Thanks for your patience With regards Sunitha Manjari Junior Research Fellow Bioinformatics Centre University of Pune Pune India From chemistry-request@server.ccl.net Fri Nov 30 05:32:42 2001 Received: from firewall.sam.co.kr ([211.118.138.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAUAWfN15557 for ; Fri, 30 Nov 2001 05:32:41 -0500 To: chemistry@server.ccl.net Subject: chemistry you are one of our winners X-Priority: 3 (Normal) Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7BIT Date: Thu, 29 Nov 2001 15:07:55 -0600 From: christop7@excite.com X-MSMail-Priority: Normal Importance: Normal Message-Id: <55yp6m.1wed8x5@yahoo.com> Dear chemistry A while back you submitted information qualifying you as one of our winners. To redeem your prize you must fill out all the blanks at the winner's site.. Click Here for details.. From chemistry-request@server.ccl.net Fri Nov 30 03:28:00 2001 Received: from arrhenius.che.chalmers.se ([129.16.90.200]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU8RxN11316 for ; Fri, 30 Nov 2001 03:27:59 -0500 Received: from arrhenius.che.chalmers.se (arrhenius.che.chalmers.se [129.16.90.200]) by arrhenius.che.chalmers.se (8.9.3/8.9.3) with ESMTP id JAA12153698; Fri, 30 Nov 2001 09:28:53 +0100 (MET) Date: Fri, 30 Nov 2001 09:28:53 +0100 From: Harald Svedung X-X-Sender: svedung@arrhenius.che.chalmers.se To: eric hu cc: chemistry@ccl.net Subject: Re: CCL:binding energy contributions from vdw and coul In-Reply-To: <20011129210325.35592.qmail@web13401.mail.yahoo.com> Message-ID: 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 fAU8S0N11319 Hi Eric and all, One way to treat intermolecular interactions in terms of first and second order terms is the NEMO potential: A. Wallqvist, G. Karlstr鰉, Chem. Scr. A 29 (1989) 131. S. Brdarski, G. Karlstr鰉, J. Phys. Chem. A 102 (1998) 8182. A mechanistic analysis there leads to the partitioning of the interaction energy into electrostatic, induction, exchange and dispersion terms. To evaluate each term, quantum chemically determined electrostatic and induction properties for the independent fragments are used. Local polarizabilities and distributed multipoles contribute to the electrostatic and induction interaction which are summed over interaction centra. The short range repulsive interaction is in principle the SCF interaction and the dispersion terms comes from London perturbation theory. I don't know if this method has been implemented for such a large system as yours, and I guess that the major problem is to choose the right interaction centra so that the resulting individual contributions becomes meaningful and somewhat stable. For what it's worth :-) /Harald Harald Svedung (PhD) phone: +46-31-7722816 Department of Chemistry fax: +46-31-167194 Physical Chemistry home phone:+46-31-240897, +46-709223206 Goeteborg University home e-mail: harald.svedung@svedung.pp.se SE-412 96 Goeteborg, Sweden. www.che.chalmers.se/~svedung/welcome.html On Thu, 29 Nov 2001, eric hu wrote: > Hi, all > > I'm working on binding energy calculation of an > antibody with its hapten. So far I've been using AMBER > and LIAISON (from Schrodinger company) to calculate > the linear response energy (LIE). I'm very interested > calculating the individual binding energy > contributions from vdw and coul interactions. I was > wondering if ther are other methods that can do this > job. Thanks. > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. > http://geocities.yahoo.com/ps/info1 > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Fri Nov 30 07:22:42 2001 Received: from mta3.263.net ([202.96.44.45]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUCMfN17640 for ; Fri, 30 Nov 2001 07:22:42 -0500 Received: by mta3.263.net (Postfix, from userid 60001) id CEAAB1C9DEA03; Fri, 30 Nov 2001 20:27:42 +0800 (CST) MIME-Version: 1.0 Message-Id: <3C077B3E.26928@mta3> Content-Type: Multipart/Alternative; boundary="Boundary-=_IgaciBDMSYnAJESMKYEwWgXXevqm" Date: Fri, 30 Nov 2001 20:27:42 +0800 (CST) From: "陈辉" To: chemistry@ccl.net Subject: =?gb2312?B?aG93IHRvIGhhbmRsZSAgYnJva2VuIHN5bW1ldHJ5Pw==?= X-Priority: 3 X-Originating-IP: [218.2.137.69] X-Mailer: Coremail2.0 Copyright Tebie Ltd., 2001 --Boundary-=_IgaciBDMSYnAJESMKYEwWgXXevqm Content-Type: Text/Html; charset="gb2312" Content-Transfer-Encoding: 8bit Dear Sir,

I have trouble when I use the Gaussian98 program to optimize
the geometry of a symmetric molecule ,the problem is the opt need
to make the symmetry lower ,the link is then die,how to handle this
problem except of using the keyword "nosymm"?

thank you.

Hui Chen
Dept chemistry
Nanjing university chemistry
P.R.China







--Boundary-=_IgaciBDMSYnAJESMKYEwWgXXevqm Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: 8bit Dear Sir, I have trouble when I use the Gaussian98 program to optimize the geometry of a symmetric molecule ,the problem is the opt need to make the symmetry lower ,the link is then die,how to handle this problem except of using the keyword "nosymm"? thank you. Hui Chen Dept chemistry Nanjing university chemistry P.R.China --Boundary-=_IgaciBDMSYnAJESMKYEwWgXXevqm-- From chemistry-request@server.ccl.net Fri Nov 30 03:54:51 2001 Received: from web13405.mail.yahoo.com ([216.136.175.63]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAU8spN12202 for ; Fri, 30 Nov 2001 03:54:51 -0500 Message-ID: <20011130085444.39203.qmail@web13405.mail.yahoo.com> Received: from [172.173.245.236] by web13405.mail.yahoo.com via HTTP; Fri, 30 Nov 2001 00:54:44 PST Date: Fri, 30 Nov 2001 00:54:44 -0800 (PST) From: quch quch Subject: Re: CCL:binding energy contributions from vdw and coul To: eric hu , chemistry@ccl.net In-Reply-To: <20011129210325.35592.qmail@web13401.mail.yahoo.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii did you really try amber? your answer is there. --- eric hu wrote: > Hi, all > > I'm working on binding energy calculation of an > antibody with its hapten. So far I've been using > AMBER > and LIAISON (from Schrodinger company) to calculate > the linear response energy (LIE). I'm very > interested > calculating the individual binding energy > contributions from vdw and coul interactions. I was > wondering if ther are other methods that can do this > job. Thanks. > > Eric > > __________________________________________________ > Do You Yahoo!? > Yahoo! GeoCities - quick and easy web site hosting, > just $8.95/month. > http://geocities.yahoo.com/ps/info1 > > > -= This is automatically added to each message by > mailing script =- > CHEMISTRY@ccl.net -- To Everybody | > CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | > Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From chemistry-request@server.ccl.net Fri Nov 30 06:02:51 2001 Received: from smtp2.ruc.dk ([130.225.220.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUB2oN16265 for ; Fri, 30 Nov 2001 06:02:50 -0500 Received: from smtprelay.ruc.dk (smtprelay.ruc.dk [130.225.220.22]) by smtp2.ruc.dk (Postfix) with ESMTP id 432C3AEAD4; Fri, 30 Nov 2001 12:02:43 +0100 (CET) Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by smtprelay.ruc.dk (8.9.3+Sun/8.9.3) with ESMTP id LAA00881; Fri, 30 Nov 2001 11:36:36 +0100 (MET) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.47); 30 Nov 01 12:02:43 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.47); 30 Nov 01 12:02:32 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: "Yi Gao" Date: Fri, 30 Nov 2001 12:02:14 +0100 Subject: CCL: TD-DFT on open shell systems Cc: chemistry@ccl.net X-Confirm-Reading-To: "Jens Spanget-Larsen" X-pmrqc: 1 Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: <4F0097F536B@virgil.ruc.dk> Yi Gao: > When I use Guassian98 to deal with open-shell systems, I found that > the TDDFT could also do work. But the Guassian's reference say TDDFT > could only deal with close-shell systems. I want to know whether the > results obtained reliable or not? Gaussian98 will perform TD-DFT calculations on open shell systems. For example, a recent TD-UB3LYP/cc-pVTZ calculation on the phenoxyl radical yielded excellent results for low energy electronic transitions [a]: TD-UB3LYP/cc-pVTZ Obs., Ar matrix cm-1(f) cm-1(eps,+/-50%) 2-B2 8300(0) 8900(-) 2-A2 19200(0.005) 16000(150) 2-B1 28900(0.029) 25200(3600) 2-A2 36300(0.042) 33900(9600) 2-B1 44000(0.150) 41800(13000) Unfortunately, the Gaussian output does not contain any precise information on the spin properties of the computed excited states. Does anybody know how to extract such information, say, the expectation value of S^2 ? Yours, Jens >--< [a] G. Radziszewski, M. Gil, A. Gorski, J. Spanget-Larsen, J. Waluk, B.J. Mroz: "Electronic states of the phenoxyl radical", J. Chem. Phys. 115, December 2001. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- From chemistry-request@server.ccl.net Fri Nov 30 08:54:14 2001 Received: from hotmail.com ([64.4.9.118]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUDsEN19342 for ; Fri, 30 Nov 2001 08:54:14 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 30 Nov 2001 05:54:02 -0800 Received: from 130.108.137.142 by lw9fd.law9.hotmail.msn.com with HTTP; Fri, 30 Nov 2001 13:54:02 GMT X-Originating-IP: [130.108.137.142] From: "Casey Kelly" To: chemistry@ccl.net Subject: Program for ZINDO/SCRF Date: Fri, 30 Nov 2001 07:54:02 -0600 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 30 Nov 2001 13:54:02.0954 (UTC) FILETIME=[78194AA0:01C179A6]
Is anyone familiar with a software program (Windows) that is capable of performing ZINDO (INDO/s) calculations in the presence of a solvent?  I would like to determine solvatochromic shifts for a series of dyes using the ZINDO method in accordance with an SCRF.  Any suggestions would be greatly appreciated and all useful replies will be summarized and submitted to the list.   
 
In regards to this question, I was directed to a software program called Argus Labs.  It is easy to install and use.  Best of all, this program is free.  It is able to incorporate an SCRF into the ZINDO method, thereby allowing determination of solvatochromic shifts for a dye.  Thanks to Mark Thompson and Jim Kress for their insight. 
 
Thank you for your help.

Casey Kelly
Graduate Student
Wright State University
Dayton, OH
 

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From chemistry-request@server.ccl.net Fri Nov 30 09:34:01 2001 Received: from fecit-gate.fecit.co.uk ([193.119.134.250]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAUEY0N20108 for ; Fri, 30 Nov 2001 09:34:01 -0500 Received: by fecit-gate.fecit.co.uk; id OAA28479; Fri, 30 Nov 2001 14:46:31 GMT Received: from suisei(192.168.101.50) by fecit-gate.fecit.co.uk via smap (V5.0) id xma028475; Fri, 30 Nov 01 14:46:13 GMT Received: from calvin.fecit.co.uk (calvin.fecit.co.uk [192.168.101.124]) by suisei.fecit.co.uk (8.6.9/8.6.9) with ESMTP id OAA11145 for ; Fri, 30 Nov 2001 14:08:42 GMT Date: Fri, 30 Nov 2001 14:33:01 +0000 (GMT) From: Andrew Horsfield X-X-Sender: To: Computational Chemistry List Subject: Argus Lab In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Does anyone know if there are any plans to port Argus Lab to platforms other than MS Windows? Cheers, Andrew From chemistry-request@server.ccl.net Fri Nov 30 12:41:21 2001 Received: from phm.utoronto.ca ([128.100.70.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUHfLN23315 for ; Fri, 30 Nov 2001 12:41:21 -0500 Received: from phm.utoronto.ca (lpk04.phm.utoronto.ca [128.100.70.180]) by phm.utoronto.ca (8.9.3+Sun/8.9.3) with ESMTP id MAA25845; Fri, 30 Nov 2001 12:41:14 -0500 (EST) Sender: william@phm.utoronto.ca Message-ID: <3C07C4C5.65169583@phm.utoronto.ca> Date: Fri, 30 Nov 2001 12:41:25 -0500 From: William Wei Reply-To: william@phm.utoronto.ca Organization: Faculty of Pharmacy, U of T X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net, amber@heimdal.compchem.ucsf.edu Subject: CMC/MD Help! Content-Type: multipart/alternative; boundary="------------CF561E072D27E162CFF1FE2B" --------------CF561E072D27E162CFF1FE2B Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear friends: I am trying to perform CMC/MD on my protein/inhibitor(s) system. I met some problems with it. I have read the paper 1 and 3 that amber manual gives. I can not find the second reference. Could anyone give me a copy of that reference? There is little guide for how to use the program Sander.MC, even the useage of this package, is it the same options and parameters with mender? and what is contents in the file MCFIL? Another question is where the result of the Free Energy Changes in the output file? I have noticed there is a part in the output file: ---------- MC summary ---------- 2 5 2 MC res: 2 counts: 260 partition: 0.7416554555 MC res: 3 counts: 0 partition: 0.2098557652 MC res: 4 counts: 0 partition: 0.0484887793 MC res: 5 counts: 0 partition: 0.0000000000 ---------- MC summary ---------- 260 are the partitions the Pi(s) mentioned in reference 3? if they are, are the Pi(s) accumulated and scaled? Can I use it to caculate the Delta delta Gbind (=-RTln(Pj/Pi)? Please forgive me for the naive question. Any hints and reply is appreciated. Thank you very much and have a nice weekend. William. -- William Wei Tel: 1-416-946-7551 (Lab.) Faculty of Pharmacy Fax: 1-416-978-8511 19 Russell Street Email: william@phm.utoronto.ca Toronto, ON. M5S 2S2, Canada william.wei@utoronto.ca --------------CF561E072D27E162CFF1FE2B Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear friends:

I am trying to perform CMC/MD on my protein/inhibitor(s) system.  I met some problems with it. I have read the paper 1 and 3 that amber manual gives. I can not find the second reference. Could anyone give me a copy of that reference?

There is little guide for how to use the program Sander.MC, even the useage of this package, is it the same options and parameters with mender? and what is contents in the file MCFIL?

Another question is where the result of the Free Energy Changes in the output file? I have noticed there is a part in the output file:
---------- MC summary ----------
    2    5    2
MC res:     2 counts:        260 partition:         0.7416554555
MC res:     3 counts:          0 partition:         0.2098557652
MC res:     4 counts:          0 partition:         0.0484887793
MC res:     5 counts:          0 partition:         0.0000000000
---------- MC summary ----------       260

are the partitions the Pi(s) mentioned in reference 3? if they are, are the Pi(s) accumulated and scaled? Can I use it to caculate the Delta delta Gbind (=-RTln(Pj/Pi)? Please forgive me for the naive question. Any hints and reply is appreciated. Thank you very much and have a nice weekend.

William. 

-- 
William Wei                    Tel: 1-416-946-7551 (Lab.)
Faculty of Pharmacy            Fax: 1-416-978-8511
19 Russell Street              Email: william@phm.utoronto.ca
Toronto, ON. M5S 2S2, Canada          william.wei@utoronto.ca
  --------------CF561E072D27E162CFF1FE2B-- From chemistry-request@server.ccl.net Fri Nov 30 11:50:00 2001 Received: from c2bapps8.btconnect.com ([193.113.209.32]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAUGnxN22480 for ; Fri, 30 Nov 2001 11:50:00 -0500 Received: from patriot (actually host host213-122-70-69.btinternet.com) by c2bapps8 with SMTP (XT-PP); Fri, 30 Nov 2001 16:49:46 +0000 From: "Roma Oakes" To: "ccl" Subject: RE: how to handle broken symmetry? Date: Fri, 30 Nov 2001 16:47:44 -0000 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0002_01C179BE.BB958510" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) In-Reply-To: <3C077B3E.26928@mta3> Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Disposition-Notification-To: "Roma Oakes" This is a multi-part message in MIME format. ------=_NextPart_000_0002_01C179BE.BB958510 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: 8bit Hi You can arrange for the calculation to continue by using one of the G98 overlays, in this case you add the keyword 'iop(2/16=3)' this tells the programe to continue the calculation with the lower symmetry Hope this helps Regards Roma -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On Behalf Of 3B;T Sent: 30 November 2001 12:28 To: chemistry@ccl.net Subject: CCL:how to handle broken symmetry? Dear Sir, I have trouble when I use the Gaussian98 program to optimize the geometry of a symmetric molecule ,the problem is the opt need to make the symmetry lower ,the link is then die,how to handle this problem except of using the keyword "nosymm"? thank you. Hui Chen Dept chemistry Nanjing university chemistry P.R.China ------=_NextPart_000_0002_01C179BE.BB958510 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Hi
 
You=20 can arrange for the calculation to continue by using one of the G98 = overlays, in=20 this case you add the keyword 'iop(2/16=3D3)'  this tells the = programe to=20 continue the calculation with the lower symmetry
 
Hope=20 this helps
 
Regards Roma
-----Original Message-----
From: Computational = Chemistry List=20 [mailto:chemistry-request@ccl.net]On Behalf Of = =B3=C2=BB=D4
Sent: 30=20 November 2001 12:28
To: chemistry@ccl.net
Subject: = CCL:how=20 to handle broken symmetry?

Dear Sir,

I have = trouble=20 when I use the Gaussian98 program to optimize
the geometry of a = symmetric=20 molecule ,the problem is the opt need
to make the symmetry lower = ,the link=20 is then die,how to handle this
problem except of using the keyword=20 "nosymm"?

thank you.

Hui Chen
Dept chemistry =
Nanjing=20 university chemistry
P.R.China







------=_NextPart_000_0002_01C179BE.BB958510-- From chemistry-request@server.ccl.net Fri Nov 30 14:58:39 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUJwdN26232 for ; Fri, 30 Nov 2001 14:58:39 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id OAA00838; Fri, 30 Nov 2001 14:58:32 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3C07DD13.5D7BF89F@cornell.edu> Date: Fri, 30 Nov 2001 14:25:07 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: I need help... Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all When I was a graduate student, my thesis advisor took us out to lunch at the end of each semester. Anyway, on one of the these lunch outings he called us all "nerds" because some of us were writing equations on the disposable table cloth. In actuality, we were discussing the fact that if one calculates the energy of a given molecule in different programs, one gets different values. The reason for this is how the zero of energy is defined. Well, my advisor was right. I am a nerd, and as such I can fix most computer related problems. However, the one that I have now has me stumped. I just upgraded my home pc from a 586/133 MHz machine running Win98 to a new Pentium4/1800 MHz machine running WinXP. Of course, I'm still trying to get hardware and software to work. I've already lost one hard drive, a tape drive and a CD-RW. Software is another story. I have/had been using HyperChem version 5. Now I find that it doesn't "work". It will open and one can try to "build" a molecule, but all you can do is add whatever the default element is to the screen. You can't change the elememt, you can't minimize, you can't even open or save files. I haven't tried reinstalling it, but I'm afraid that probably won't help. Does anybody have any advice or suggestions besides upgrading to a newer version (which I can't afford)? Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri Nov 30 18:56:01 2001 Received: from cheetah.it.wsu.edu (root@[134.121.1.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAUNu0N32578 for ; Fri, 30 Nov 2001 18:56:00 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by cheetah.it.wsu.edu (8.11.6/8.11.6) with SMTP id fAUNtql29701; Fri, 30 Nov 2001 15:55:52 -0800 (PST) Message-ID: <000901c179fa$8b194ac0$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Dr. Richard L. Wood" , References: <3C07DD13.5D7BF89F@cornell.edu> Subject: Re: CCL:I need help... Date: Fri, 30 Nov 2001 15:55:52 -0800 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 Richard, Make sure you have the parallel port (and service) enabled. I had the same problem regarding saving files in HyperChem and it turned out I had disabled my parallel port in the BIOS and as such the HyperChem service (software dongle) could not start. I even go so far as installing dummy printer drivers to use LPT1 so WIN2K keeps the parallel port service started (maybe overkill but the solution makes HyperChem work). Good luck! Respectfully, Phil ----- Original Message ----- From: "Dr. Richard L. Wood" To: Sent: Friday, November 30, 2001 11:25 AM Subject: CCL:I need help... > Hi all > > When I was a graduate student, my thesis advisor took us out to lunch at > the end of each semester. > Anyway, on one of the these lunch outings he called us all "nerds" > because some of us were writing > equations on the disposable table cloth. In actuality, we were > discussing the fact that if one > calculates the energy of a given molecule in different programs, one > gets different values. The reason for > this is how the zero of energy is defined. > > Well, my advisor was right. I am a nerd, and as such I can fix most > computer related problems. However, > the one that I have now has me stumped. > > I just upgraded my home pc from a 586/133 MHz machine running Win98 to a > new Pentium4/1800 MHz > machine running WinXP. Of course, I'm still trying to get hardware and > software to work. I've already > lost one hard drive, a tape drive and a CD-RW. Software is another > story. > > I have/had been using HyperChem version 5. Now I find that it doesn't > "work". It will open and one can try > to "build" a molecule, but all you can do is add whatever the default > element is to the screen. You can't change the elememt, you can't > minimize, you can't even open or save files. I haven't tried > reinstalling it, > but I'm afraid that probably won't help. > > Does anybody have any advice or suggestions besides upgrading to a newer > version (which I can't afford)? > > Thanks, > Richard > > -- > Richard L. Wood, Ph. D. > Physical/Computational Chemist > Post-doctoral Associate > Department of Food Science > 120 Stocking Hall > Cornell University, Ithaca, NY 14853 > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > >