From chemistry-request@ccl.net Fri Jul 25 08:53:33 2003 Received: from facstaff.wesleyan.edu (facstaff.wesleyan.edu [129.133.1.61]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6PCrW47019090 for ; Fri, 25 Jul 2003 08:53:33 -0400 Received: from facstaff.wesleyan.edu (localhost [127.0.0.1]) by facstaff.wesleyan.edu (8.12.9/8.12.6) with ESMTP id h6PCrMAD009100 for ; Fri, 25 Jul 2003 08:53:22 -0400 (EDT) Received: from localhost (yliu@localhost) by facstaff.wesleyan.edu (8.12.9/8.12.6/Submit) with ESMTP id h6PCrMoN009088 for ; Fri, 25 Jul 2003 08:53:22 -0400 (EDT) Date: Fri, 25 Jul 2003 08:53:22 -0400 (EDT) From: Yongxing Liu To: chemistry..at..ccl.net Subject: Latest Experience with PC 3D Display Hardware Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-ECS-MailScanner: Found to be clean Hi, I am wondering if anyone can share with me your latest experience with PC (Desktop/Laptop, Windows/Linux) 3D display hardware (Graphics Card, Glasses and Monitor etc). Thanks a lot in advance. Yongxing Liu From chemistry-request@ccl.net Thu Jul 24 23:44:07 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6P3i647001840 for ; Thu, 24 Jul 2003 23:44:06 -0400 Received: from email.unb.ca (root..at..newpop.unb.ca [131.202.3.46]) by mailserv.unb.ca (8.12.6/8.12.6) with ESMTP id h6OInikY031820; Thu, 24 Jul 2003 15:49:44 -0300 Received: from [131.202.130.26] (HELO webmail1) by email.unb.ca (CommuniGate Pro SMTP 4.0.6) with ESMTP id 13955015; Thu, 24 Jul 2003 15:49:44 -0300 X-WebMail-UserID: l72k6 Date: Thu, 24 Jul 2003 15:49:36 -0300 Sender: Robert Flight From: Robert Flight To: Computational Chemistry List , sa.cosco..at..virgilio.it X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:Adding counterions on a protein Message-ID: <3F22D21E@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=1.5, required 5, DEAR_SOMEBODY, FROM_HAS_MIXED_NUMS, SPAM_PHRASE_03_05) Hi Sandro, I dont know about scripts, but I do know that GRID is supposedly capable of calculating interaction energies and finding energetically favorable sites for counterions in proteins. I havent tried it myself, but I have seen it listed in the user manual. http://www.moldiscovery.com/docs/grid21/index.html http://www.moldiscovery.com/soft_grid.php Cheers, -Robert >===== Original Message From sa.cosco..at..virgilio.it ===== >Dear All >Does anybody know if there is an efficient script to add counterions on >a protein in a random way? >Actually, I tried to perform it with InsightII and Sybyl scripts but they >have been constructed for nucleotides. Would it be possible to get scripts >properly modified for proteins working with InsightII or Sybyl programs? >Thanks in advance for your help. >Best regards >Sandro > > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: line >and send your message to: CHEMISTRY..at..ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST..at..ccl.net >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl..at..ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: robert.flight..at..unb.ca ******************************** "People think it must be fun to be a super genius, but they don't realize how hard it is to put up with all the idiots in the world." -Calvin from Calvin & Hobbes From chemistry-request@ccl.net Fri Jul 25 00:04:36 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6P44a47002197 for >ccl.net>; Fri, 25 Jul 2003 00:04:36 -0400 Received: from connie.summerhill (syr-24-58-0-128.twcny.rr.com [24.58.0.128]) by cornell.edu (8.9.3p2/8.9.3) with ESMTP id UAA14934 for >ccl.net>; Thu, 24 Jul 2003 20:42:45 -0400 (EDT) Subject: CCl: Gaussian and Field keyword and Optimizations From: Connie Chang >cornell.edu> To: chemistry<>ccl.net Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Mailer: Ximian Evolution 1.0.8 (1.0.8-10) Date: 24 Jul 2003 20:42:22 -0400 Message-Id: <1059093747.991.1.camel@connie> Mime-Version: 1.0 Hi -- I'm trying to optimize a molecule in the presence of a field using Gaussian. Why is it that Gaussian won't allow me to optimize using PM3? But it seems to let me optimize in the presence of a field with HF? In light of the fact that Gaussian won't let me optimize in the presence of a field with PM3. Does that mean that a single point calculation with PM3 and in the presence of a Field also has no meaning????!!! Thanks! :) Connie From chemistry-request@ccl.net Fri Jul 25 04:25:40 2003 Received: from mail9.messagelabs.com (mail9.messagelabs.com [194.205.110.133]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6P8Pd47010669 for >server.ccl.net>; Fri, 25 Jul 2003 04:25:40 -0400 X-VirusChecked: Checked X-Env-Sender: Daniel.Tackley<>avecia.com X-Msg-Ref: server-29.tower-9.messagelabs.com!1059121533!448568 X-StarScan-Version: 5.0.7; banners=-,-,- Received: (qmail 23740 invoked from network); 25 Jul 2003 08:25:33 -0000 Received: from unknown (HELO wwwhx980.avecia.com) (217.205.231.98) by server-29.tower-9.messagelabs.com with SMTP; 25 Jul 2003 08:25:33 -0000 Received: from wwwhx109.avecia.com by wwwhx980.avecia.com via smtpd (for mail9.messagelabs.com [194.205.110.133]) with ESMTP; Fri, 25 Jul 2003 09:29:09 +0100 Received: from [10.156.1.180] (unverified) by wwwhx109.avecia.com (Content Technologies SMTPRS 4.2.10) with SMTP id >wwwhx109.avecia.com> for >server.ccl.net>; Fri, 25 Jul 2003 09:29:59 +0100 Received: from avecia.com by [10.156.1.180] via smtpd (for wwwhx109.avecia.com [10.156.1.109]) with SMTP; Fri, 25 Jul 2003 09:28:40 +0100 Received: by UKHX48 with Internet Mail Service (5.5.2653.19) id ; Fri, 25 Jul 2003 09:25:27 +0100 Message-ID: <67DFB9481700D111900E00805F59F86104C04509@UKHX14> From: Tackley Daniel R >avecia.com> To: "Comp Chem Mailing List (E-mail)" >server.ccl.net> Subject: G98 Error - "Overflow in Choose" Date: Fri, 25 Jul 2003 09:25:25 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" Dear All, Has anyone ever seen and solved this error in G98? I'm trying to run a single point SCF using DFT (functional makes no difference to generating the error) in conjunction with the WTBS "Well-Tempered Basis Set" for Iridium obtained from the EMSL Basis Set Library. Any suggestions? (Enter C:\G98W\l502.exe) IExCor= 408 DFT=T Ex=B Corr=PW91 ScaHFX= 0.0000 ScaDFX= 1.0000 1.0000 1.0000 1.0000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 Using DIIS extrapolation. Closed shell SCF: Requested convergence on RMS density matrix=1.00D-04 within1000 cycles. Requested convergence on MAX density matrix=1.00D-02. Requested convergence on energy=5.00D-05. Virtual orbitals will be shifted by 0.200 hartree. Two-electron integral symmetry not used. Keep R1 and R2 integrals in memory in canonical form, NReq= 3319928. IEnd= 1010272 IEndB= 1010272 NGot= 104857600 MDV= 103681835 LenX= 103681835 Symmetry not used in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 1 IRICut= 1 DoRegI=T DoRafI=F ISym2E= 0 JSym2E=0. Overflow in Choose. Error termination via Lnk1e in C:\G98W\l502.exe. Job cpu time: 0 days 0 hours 20 minutes 5.0 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 11 Scr= 1 Many Thanks, Daniel Tackley -- Dr Daniel Tackley Computational Chemistry Group Avecia Ltd Manchester UK Tel: +44 (0)161 721 2541 Email: daniel.tackley<>avecia.com From chemistry-request@ccl.net Thu Jul 24 23:51:30 2003 Received: from sandmail01.sd.accelrys.com (fw1.sd.accelrys.com [209.120.169.30]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6P3pT47001960 for >ccl.net>; Thu, 24 Jul 2003 23:51:29 -0400 In-Reply-To: <3F1662620000CF3D<>ims1b.cp.tin.it> To: sa.cosco<>virgilio.it Cc: chemistry<>ccl.net Subject: Re: CCL:Adding counterions on a protein MIME-Version: 1.0 X-Mailer: Lotus Notes Release 6.0.1CF1 March 04, 2003 Message-ID: >accelrys.com> From: Ken Butenhof >accelrys.com> Date: Thu, 24 Jul 2003 14:43:21 -0400 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 6.0.2CF1|June 9, 2003) at 07/24/2003 20:51:28, Serialize complete at 07/24/2003 20:51:28 Content-Type: multipart/alternative; boundary="=_alternative 0066D0DD85256D6D_=" This is a multipart message in MIME format. --=_alternative 0066D0DD85256D6D_= Content-Type: text/plain; charset="US-ASCII" Hello Sandro, There are many scripts in Accelrys' on-line BCL script library for use with Insight II. One of these scripts is called counterion.bcl. This script will place counterions suitable for use with several different force fields for charged residues in RNA/DNA or PEPTIDES. The script uses a template recognition method to determine a suitable initial placement. Additional recognition templates can be added. Be sure to read the scripts header information closely for any dependant scripts that will need to be downloaded with it. The main script's name is counterion.bcl. The link is http://www.accelrys.com/support/life/scripts/bcl_lib.html Best wishes, Ken _______________________________________________ Kenneth Butenhof phone: 800 756-4674 Principal Scientist email: kenb<>accelrys.com Accelrys Inc. web: www.accelrys.com sa.cosco<>virgilio.it Sent by: "Computational Chemistry List" >ccl.net> 07/24/2003 12:56 PM To chemistry<>ccl.net cc Subject CCL:Adding counterions on a protein Dear All Does anybody know if there is an efficient script to add counterions on a protein in a random way? Actually, I tried to perform it with InsightII and Sybyl scripts but they have been constructed for nucleotides. Would it be possible to get scripts properly modified for proteins working with InsightII or Sybyl programs? Thanks in advance for your help. Best regards Sandro -= This is automatically added to each message by mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY<>ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jkl<>ccl.net (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --=_alternative 0066D0DD85256D6D_= Content-Type: text/html; charset="US-ASCII"
Hello Sandro,

There are many scripts in Accelrys' on-line BCL script library for use with Insight II.  One of these scripts is called counterion.bcl.  This script will place counterions suitable for use with several different force fields for charged residues in RNA/DNA or PEPTIDES.  The script uses a template recognition method to determine a suitable initial placement.  Additional recognition templates can be added.  Be sure to read the scripts header information closely for any dependant scripts that will need to be downloaded with it.  The main script's name is counterion.bcl.  The link is
http://www.accelrys.com/support/life/scripts/bcl_lib.html

Best wishes,

Ken
_______________________________________________
Kenneth Butenhof          phone:  800 756-4674
Principal Scientist          email:    kenb<>accelrys.com
Accelrys Inc.                   web:     www.accelrys.com


sa.cosco<>virgilio.it
Sent by: "Computational Chemistry List" <chemistry-request<>ccl.net>

07/24/2003 12:56 PM

To
chemistry<>ccl.net
cc
Subject
CCL:Adding counterions on a protein





Dear All
Does anybody know if there is an efficient script to add counterions on
a protein in a random way?
Actually, I tried to perform it with InsightII and Sybyl scripts but they
have been constructed for nucleotides. Would it be possible to get scripts
properly modified for proteins working with InsightII or Sybyl programs?
Thanks in advance for your help.
Best regards
Sandro



-= This is automatically added to each message by mailing script =-
To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
and send your message to:  CHEMISTRY<>ccl.net

Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net
HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs

If your mail is bouncing from CCL.NET domain send it to the maintainer:
Jan Labanowski,  jkl<>ccl.net (read about it on CCL Home Page)
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--=_alternative 0066D0DD85256D6D_=-- From chemistry-request@ccl.net Fri Jul 25 00:25:39 2003 Received: from adm3.ims.u-tokyo.ac.jp (adm3.ims.u-tokyo.ac.jp [157.82.98.26]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h6P4Pb47002446 for >ccl.net>; Fri, 25 Jul 2003 00:25:38 -0400 Received: (qmail 16160 invoked by uid 7794); 25 Jul 2003 13:25:29 +0900 Received: from mdehoon<>ims.u-tokyo.ac.jp by adm3 by uid 7791 with qmail-scanner-1.10 (. Clear:0. Processed in 0.427117 secs); 25 Jul 2003 04:25:29 -0000 Received: from lavender.ims.u-tokyo.ac.jp (HELO ims.u-tokyo.ac.jp) (133.103.74.218) by adm3.ims.u-tokyo.ac.jp with SMTP; 25 Jul 2003 13:25:28 +0900 Message-ID: <3F20B19E.9020807<>ims.u-tokyo.ac.jp> Date: Fri, 25 Jul 2003 13:27:10 +0900 From: Michiel Jan Laurens de Hoon >ims.u-tokyo.ac.jp> User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: nl, en, en-us, hu, ja, de, fr MIME-Version: 1.0 To: chemistry<>ccl.net Subject: Amber94 force field parameters for Saquinavir, Indinavir Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi, I am using Konrad Hinsen's Molecular Modeling Toolkit to estimate changes caused by mutations in the HIV genome in the binding energy between the HIV protease and the Indinavir and Saquinavir protease inhibitors. Using Modeller, I can create PDB files with the estimated structure of a mutated HIV protease complexed to the protease. To calculate the interaction energy, I would need the Amber94 force field parameters for the inhibitor. Are such parameters available somewhere? I didn't find them on the Amber web site, though I would think that Indinavir and Saquinavir are well-studied molecules. Is it possible to mock up the interaction between the protease and the inhibitor? Something quick and dirty is fine for what I am doing. Many thanks in advance, Michiel de Hoon, Univsersity of Tokyo. -- Michiel de Hoon, Assistant Professor University of Tokyo, Institute of Medical Science Human Genome Center 4-6-1 Shirokane-dai, Minato-ku Tokyo 108-8639 Japan http://bonsai.ims.u-tokyo.ac.jp/~mdehoon From chemistry-request@ccl.net Fri Jul 25 14:47:01 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6PIl047032650 for ; Fri, 25 Jul 2003 14:47:01 -0400 Received: from dopey (dopey.ccmr.cornell.edu [128.84.241.121]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id OAA01087 for ; Fri, 25 Jul 2003 14:47:01 -0400 (EDT) Message-ID: <001101c352dd$22496030$79f15480.-at-.ccmr.cornell.edu> From: "Connie Chang" To: Subject: CCL: Gaussian checkpoint files Date: Fri, 25 Jul 2003 14:47:01 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C352BB.9B0F50A0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C352BB.9B0F50A0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi -- Is there any way to get an initial orbital guess from a checkpoint file = using Guess=3DRead and at the same time *not* write to a checkpoint = file? I have many jobs reading from the same checkpoint file and would rather = not have to make 420 copies of the same large checkpoint file for each = job. Thanks! Connie ------=_NextPart_000_000E_01C352BB.9B0F50A0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi --
 
Is there any way to get an initial = orbital guess=20 > from a checkpoint file using Guess=3DRead and at the same time *not* = write to a=20 checkpoint file?
 
I have many jobs reading from the same = checkpoint=20 file and would rather not have to make 420 copies of the same large = checkpoint=20 file for each job.
 
Thanks!
Connie
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