From chemistry-request@server.ccl.net Tue Mar 26 05:37:06 2002 Received: from mail.unime.it ([192.167.101.15]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QAb6p02539 for ; Tue, 26 Mar 2002 05:37:06 -0500 Received: from pharma.unime.it (pharma.unime.it [192.167.106.20]) by mail.unime.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0GTK00IJCTHI3B@mail.unime.it> for chemistry@ccl.net; Tue, 26 Mar 2002 11:36:55 +0100 (MET) Received: from bunker (mlbarreca.unime.it [192.167.106.99]) by pharma.unime.it (8.11.6/linuxconf) with ESMTP id g2QAaq513890 for ; Tue, 26 Mar 2002 11:36:53 +0100 Date: Tue, 26 Mar 2002 11:37:43 +0100 From: maria letizia barreca Subject: SCORE To: chemistry@ccl.net Message-id: <000201c1d4b2$42f03430$636aa7c0@bunker> MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 X-Mailer: Microsoft Outlook, Build 10.0.2627 Content-type: multipart/alternative; boundary="Boundary_(ID_1Js0HGmW51CL+wuPgZsAYQ)" Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal X-MailScanner: Found to be clean This is a multi-part message in MIME format. --Boundary_(ID_1Js0HGmW51CL+wuPgZsAYQ) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7BIT Dear CClers, I would like to know if SCORE(for estimating the binding affinity of protein-ligand complex)is still freely distributed and how to obtain it. I wrote several times to the correspondents indicated in the SCORE web page, but I got my emails back. Regards, Maria Letizia ----------------------------------------------- Maria Letizia Barreca, Ph.D. Dipartimento Farmaco-Chimico Universita'degli Studi di Messina Viale Annunziata 98168 MESSINA ITALY Phone: +39 090 6766464 Fax: +39 090 355613 email: barrecal@pharma.unime.it --Boundary_(ID_1Js0HGmW51CL+wuPgZsAYQ) Content-type: text/html; charset=iso-8859-1 Content-transfer-encoding: quoted-printable

Dear CClers,

I would like to know if SCORE(for estimating the binding affinity of = protein-ligand complex)is still freely distributed and how to obtain it.

I wrote several times to the correspondents indicated in the SCORE web page, but I got my emails back.

 

Regards,

 

Maria Letizia

 

-----------------------------------------------

Maria Letizia Barreca, = Ph.D.

Dipartimento = Farmaco-Chimico

Universita'degli Studi di = Messina

Viale Annunziata 98168 MESSINA = ITALY

Phone: +39 090 = 6766464

Fax:=A0=A0 = +39 090 355613

email: = barrecal@pharma.unime.it

 

--Boundary_(ID_1Js0HGmW51CL+wuPgZsAYQ)-- From chemistry-request@server.ccl.net Tue Mar 26 12:53:45 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QHrip10306 for ; Tue, 26 Mar 2002 12:53:45 -0500 Received: from silicon.chem.ucla.edu (silicon.chem.ucla.edu [169.232.135.10]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id g2QHrcm12390; Tue, 26 Mar 2002 09:53:38 -0800 (PST) Received: from Laurence.mbi.ucla.edu (pc-ll.chem.ucla.edu [128.97.35.245]) by silicon.chem.ucla.edu (8.11.1/8.11.1) with ESMTP id g2QHreQ27437; Tue, 26 Mar 2002 09:53:40 -0800 (PST) Message-Id: <5.1.0.14.2.20020326094902.02fe71b0@mbi.ucla.edu> X-Sender: lavelle@mbi.ucla.edu X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Mar 2002 09:53:34 -0800 To: "Support" , "CCL" From: Laurence Lavelle Subject: Chem 3D Ultra 7.0 as a Gaussian interface. In-Reply-To: <2002322_@TLM196749_@TLM> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Rich, Thank for your prompt and straight forward reply. However I am surprised that bugs leading to incorrect bond lengths when using Chem 3D as a Gaussian interface was not given higher priority three years and two versions ago. I look forward to using version 8. Sincerely, Laurence Lavelle At 08:52 AM 3/22/2002 -0500, Support wrote: >Just looking back at our correspondence with you, I have found that the >three bugs you have reported and other suggestions have not been addressed >in 7.0. The main things that have been added to Chem3D since 5.0 are a >GAMESS interface and Tinker. Some bugs have been fixed, too. R&D is >aware of the items you have reported and we hope to address them in a >future version, but it is not clear when that will be. > >Regards, > >Rich Talbot >Director, Technical Support >CambridgeSoft >support@cambridgesoft.com > > >Do you want to know when software patches are available, the latest >product problems and solutions, facts, tricks and tips, tidbits and >more? Then sign up for our FREE technical support newsletter at: >http://www.cambridgesoft.com/support/nl/new.cfm > > > > >-----Original Message----- > >From: Laurence Lavelle[lavelle@mbi.ucla.edu] > >Date: Thursday, March 21, 2002 06:54 PM > >To: CCL[chemistry@ccl.net] > >Subject: Chem 3D Ultra 7.0 as a Gaussian interface. > > > > > >I tried using Chem 3D version 5 as a Gaussian interface some time back > >but > >it was full of bugs. > > > >Anyone having successful use of Chem 3D Ultra 7.0 as a Gaussian > >interface ? > >In particular for pdb files ? > > > >Thanks, > >Laurence > > > > > > From chemistry-request@server.ccl.net Tue Mar 26 11:54:40 2002 Received: from ns2.tudelft.nl ([130.161.180.65]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QGsdp09387 for ; Tue, 26 Mar 2002 11:54:39 -0500 Received: from listserv.tudelft.nl (listserv.tudelft.nl [130.161.180.33]) by mailhost1.tudelft.nl (PMDF V6.0-025 #40924) with ESMTP id <0GTL00K6WAYXVA@mailhost1.tudelft.nl> for chemistry@ccl.net; Tue, 26 Mar 2002 17:54:33 +0100 (MET) Received: from stm-ltc2.dct.tudelft.nl (stm-ltc2.dct.tudelft.nl [130.161.196.198]) by listserv.tudelft.nl (8.10.2+Sun/8.10.2) with ESMTP id g2QGsT522356 for ; Tue, 26 Mar 2002 17:54:33 +0100 (MET) Received: from STM-LTC2/SpoolDir by stm-ltc2.dct.tudelft.nl (Mercury 1.47) ; Tue, 26 Mar 2002 17:54:32 +0000 (MET-1MEST) Received: from SpoolDir by STM-LTC2 (Mercury 1.47); Tue, 26 Mar 2002 17:54:28 +0000 (MET-1MEST) Date: Tue, 26 Mar 2002 17:54:27 +0100 From: Martijn Zwijnenburg Subject: oniom calc To: chemistry@ccl.net Message-id: <3CA0B5D2.28843.4FBE6D@localhost> MIME-version: 1.0 X-Mailer: Pegasus Mail for Win32 (v3.12c) Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Priority: normal 0100,0100,0100Hi, When we're performing oniom calcs, using G98, the calculation always crashes due to the fact that in the high-level part of the calculation the multiplicity doesn't equal the input value of 1. Looking at the output it seems that gaussian98 doesn't add the necessary terminating hydrogens. Example we did a calculation on trifluoromethylsilane (CH3F3Si) wherein we treated the trifluoromethyl part on a medium (AM1) level whereas the rest of molecule was calculated on the High (DFT) level. Courier New%Chk=oniom_test #P trackio # opt ONIOM(B3LYP/sto-3g:AM1) # NoSymm oniom_test job oniom_test archiving 0 1 SI -0.354 -0.184 0.688 High C -1.345 -0.451 -0.882 Medium F -1.135 -1.670 -1.475 Medium F -2.703 -0.384 -0.701 Medium F -1.082 0.464 -1.870 Medium H -0.901 0.971 1.390 High H 1.037 0.052 0.322 High H -0.466 -1.381 1.514 High ArialThe first AM1 calculation gives no problems but before the DFT part of the oniom calc starts for the first time the programme crashes with the following error message: Courier New ONIOM: generating new system at layer 1 ONIOM: saving gridpoint 3 ONIOM: restoring gridpoint 9 Leave Link 120 at Tue Mar 26 12:12:02 2002, MaxMem= 6291456 cpu: 0.0 (Enter /usr/local/g98/l301.exe) Standard basis: STO-3G (5D, 7F) The combination of multiplicity 1 and 17 electrons is impossible. Error termination via Lnk1e in /usr/local/g98/l301.exe. Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 ArialThe 17 electrons are just the silicon and the three hydrogens. Apparently the terminating hydrogen is not added by the program. Does anybody know what is going wrong here and how to fix the problem? Any suggestions are more then welcome. cheers, Martijn Courier New ------------------------------------------------------------------------- Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis Delft University of Technology Julianalaan 136 2628 BL Delft The Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock From chemistry-request@server.ccl.net Tue Mar 26 14:56:12 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QJuBp13194 for ; Tue, 26 Mar 2002 14:56:11 -0500 Received: (from kenb@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g2QL3lm23088 for chemistry@ccl.net; Tue, 26 Mar 2002 13:03:47 -0800 Received: from iris105.sd.accelrys.com (iris105.sd.accelrys.com [172.30.40.105]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g2QL3kV23079 for <@nmh-inner.sd.accelrys.com:chemistry@ccl.net>; Tue, 26 Mar 2002 13:03:47 -0800 Received: from kenbutenhof-pc.accelrys.com by iris105.sd.accelrys.com via ESMTP (980427.SGI.8.8.8/930416.SGI) for id LAA06910; Tue, 26 Mar 2002 11:55:59 -0800 (PST) Message-Id: <5.1.0.14.2.20020326135642.01ed7e80@172.30.45.77> X-Sender: kenb@172.30.45.77 X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Tue, 26 Mar 2002 14:37:43 -0500 To: chemistry@ccl.net From: Ken Butenhof Subject: Re: Question on charges in CVFF on CCL Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_109215463==_.ALT" --=====================_109215463==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Hello CCL'ers, In Insight II for all force fields except CFF, assignment of charges (and atom types) to each atom is done with the "Potentials" parameter block, which is accessed from the "FF" icon. The Insight program assigns atom types and partial charges to each atom in the structure based on information in a residue library file (.rlb) if the residue is known or (if not found in a residue library file) from the bond increments found in the force field file based on the atom types. The charge values present in the residue library file and the bond increments in the force field file (.frc) are derived from experimental (usually crystallographic) data and quantum mechanical modelling. The purpose of using a bond increment scheme for residues not in the residue library is that the local bonded environment (as described by the atom types) determines the atom centered charge. The Gasteiger method first determines the overall charge of the system and then distributes that charge throughout the molecule (the Gasteiger method is available for use with Discover in Cerius2). Note that CVFF was developed to reproduce peptide and protein properties. The CFF force field has far greater support for highly funtionalized small molecules. This information is available to all Accelrys users at http://www.accelrys.com/doc. Ken >Dear all the CCLers: > I am a user of InsightII of Accelrys(former MSI). When I perform >comutations, such as molecular minization or dynamics,I often use CVFF >force field. I always >use FF (ForceField). This command is activated on the left side by >clicking on the FF >button. Then select Forcefield/Potentials and make sure that all of the >settings as >follows. > Potential Action [Fix] > > Partial Charge Action [Fix] > > Formal Charge Action [Fix or Accept] > > My question is how the partial charges of my molecules are computed? >In my opinion,the partial charges are part of the CVFF force field. When CVFF >is used, thepartial charges are automatically loaded from the system file. >This is >quite different from MM2 (Tripos) method which often calculate partial >charge through >Gasteiger-Huckel method for small molecules.Is this so? I have referred >several papers, >but find no how the charges are computed. Kenneth Butenhof, Ph. D. phone: 800 756-4674 Principle Scientist email: kenb@accelrys.com Life Science Support web: www.accelrys.com/support Accelrys --=====================_109215463==_.ALT Content-Type: text/html; charset="us-ascii" Hello CCL'ers,

In Insight II for all force fields except CFF, assignment of charges (and atom types) to each atom is done with the "Potentials" parameter block, which is accessed from the "FF" icon.  The Insight program assigns atom types and partial charges to each atom in the structure based on information in a residue library file (.rlb) if the residue is known or (if not found in a residue library file) from the bond increments found in the force field file based on the atom types.  The charge values present in the residue library file and the bond increments in the force field file
(.frc) are derived from experimental (usually crystallographic) data and quantum mechanical modelling.  The purpose of using a bond increment scheme for residues not in the residue library is that the local bonded environment (as described by the atom types) determines the atom centered charge.  The Gasteiger method first determines the overall charge of the system and then distributes that charge throughout the molecule (the Gasteiger method is available for use with Discover in Cerius2).  Note that CVFF was developed to reproduce peptide and protein properties.   The CFF force field has far greater support for highly funtionalized small molecules.
This information is available to all Accelrys users at http://www.accelrys.com/doc.

Ken

Dear all the CCLers:
    I am a user of InsightII of Accelrys(former MSI). When I perform
comutations, such as molecular minization or dynamics,I often use CVFF force field. I always
use FF (ForceField). This command is activated on the left side by clicking on the FF
button. Then select Forcefield/Potentials and make sure that all of the settings as
follows.
            Potential Action [Fix]

            Partial Charge Action [Fix]

            Formal Charge Action [Fix or Accept]

    My question is how the partial charges of my molecules are computed?
In my opinion,the partial charges are part of the CVFF force field. When CVFF
is used, thepartial charges are automatically loaded from the system file. This is
quite different from MM2 (Tripos) method which often calculate partial charge through
Gasteiger-Huckel method for small molecules.Is this so? I have referred several papers,
but find no how the charges are computed.



Kenneth Butenhof, Ph. D.        phone: 800 756-4674
Principle Scientist             email: kenb@accelrys.com
Life Science Support            web:  www.accelrys.com/support
Accelrys --=====================_109215463==_.ALT-- From chemistry-request@server.ccl.net Tue Mar 26 09:54:20 2002 Received: from mail1.rrz.Uni-Koeln.DE ([134.95.100.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QEsKp07212 for ; Tue, 26 Mar 2002 09:54:20 -0500 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:2897@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.12.2/8.12.2) with ESMTP id g2QEs7mY027124 for ; Tue, 26 Mar 2002 15:54:07 +0100 (MET) Received: from localhost (acp64@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) with SMTP id PAA11502 for ; Tue, 26 Mar 2002 15:54:05 +0100 (MET) X-Authentication-Warning: campfire.rrz.Uni-Koeln.DE: acp64 owned process doing -bs Date: Tue, 26 Mar 2002 15:54:05 +0100 (MET) From: Johannes Weber To: chemistry@ccl.net Subject: g98: TD-DFT geometry optimizations ? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 X-Virus-Scanned: by amavisd-milter (http://amavis.org/) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g2QEsKp07213 Dear CCL members, I have a Gaussian 98 related question: According to the g98 users manual (p. 155, TD keyword) it should be possible to do Time Dependent DFT geometry optimizations of the N-th excited state using the Root=N option. However, I canīt find a proper input. The easiest input line #P TD=(Root=1) B3LYP/STO-3G Test DENSITY OPT=Z-Matrix leads to an error in link 1002: (Enter /vol/chemie/libexec/g98.A9/g98/l1002.exe) Minotr: Closed-shell wavefunction. Cannot mix post-SCF and DFT. Error termination via Lnk1e in /vol/chemie/libexec/g98.A9/g98/l1002.exe. I played around with several other options, tried to do the job in a two step procedure, like it is described for the CIS method in Forsman/Frischīs "Exploring Chemistry with Electronic Structure Methods", all without success. Is it possible to do these calculations? Anybody out there with experience in this topic? The ultimate goal would be to perform a normal mode frequency calculation for excited states within the TD-DFT formalism. Regards, :-)ohannes. ---------------------------------------------------------------------- | Johannes Weber | Email: | | Universitaet zu Koeln | Johannes.Weber@uni-koeln.de | | Institut fuer Physikalische Chemie | | | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4812 | | Luxemburger Str. 116 | fax: 0049-(0)221-470-5144 | | 50939 Koeln | | ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Mar 26 17:31:22 2002 Received: from electra.cc.umanitoba.ca ([130.179.16.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QMVMp16037 for ; Tue, 26 Mar 2002 17:31:22 -0500 Received: from hultin (hultin.chem.umanitoba.ca [130.179.48.60]) by electra.cc.umanitoba.ca (8.12.2/8.12.2) with SMTP id g2QMVCSu007914 for ; Tue, 26 Mar 2002 16:31:12 -0600 (CST) From: "Phil Hultin" To: "Computational Chemistry List" Subject: Re: Gaussian ONIOM problem Date: Tue, 26 Mar 2002 16:31:12 -0600 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-DCC-UofM-Metrics: electra 1032; Body=1 Fuz1=1 Fuz2=1 Martijn Zwijnenburg inquired about the failure of an ONIOM calculation using G98. I just encountered the same problem with my first attempts at using ONIOM. I found that it was necessary to explicitly define the "replace-atom" in the input file for those atoms which were at the boundary between higher and lower levels. The Gaussian manual states that defining a replace-atom is an option, but this apparently is NOT the case. So, Martijn, try modifying your input file to this: %Chk=oniom_test #P trackio # opt ONIOM(B3LYP/sto-3g:AM1) # NoSymm oniom_test job oniom_test archiving 0 1 SI -0.354 -0.184 0.688 High C -1.345 -0.451 -0.882 Medium H F -1.135 -1.670 -1.475 Medium F -2.703 -0.384 -0.701 Medium F -1.082 0.464 -1.870 Medium H -0.901 0.971 1.390 High H 1.037 0.052 0.322 High H -0.466 -1.381 1.514 High Dr. Philip G. Hultin Associate Department Head and Associate Professor of Chemistry University of Manitoba Winnipeg, MB, Canada R3T 2N2 (vox) 204-474-9814 (fax) 204-474-7608 mailto:hultin@cc.umanitoba.ca http://www.umanitoba.ca/chemistry/ From chemistry-request@server.ccl.net Tue Mar 26 18:03:22 2002 Received: from bico-de-lacre.iqm.unicamp.br ([143.106.51.234]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QN3Lp17341 for ; Tue, 26 Mar 2002 18:03:21 -0500 Received: by bico-de-lacre.iqm.unicamp.br (Postfix, from userid 1001) id 89C8A19A3; Tue, 26 Mar 2002 20:03:12 -0300 (BRT) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Message-ID: <15520.65072.370736.984055@bico-de-lacre.iqm.unicamp.br> Date: Tue, 26 Mar 2002 20:03:12 -0300 From: Ataualpa Albert Carmo Braga To: chemistry@ccl.net Subject: Re: CCL:oniom calc In-Reply-To: <3CA0B5D2.28843.4FBE6D@localhost> References: <3CA0B5D2.28843.4FBE6D@localhost> X-Mailer: VM 6.76 under Emacs 20.6.1 Reply-To: atabraga@iqm.unicamp.br Sender: atabraga@iqm.unicamp.br X-URL: http://www.iqm.unicamp.br Hi, Try this: %Chk=oniom_test #P trackio # opt ONIOM(B3LYP/sto-3g:AM1) # NoSymm oniom_test job oniom_test archiving 0 1 SI -0.354 -0.184 0.688 High C -1.345 -0.451 -0.882 Medium H F -1.135 -1.670 -1.475 Medium F -2.703 -0.384 -0.701 Medium F -1.082 0.464 -1.870 Medium H -0.901 0.971 1.390 High H 1.037 0.052 0.322 High H -0.466 -1.381 1.514 High ------ Ata. on Tuesday, 26 Mar 2002 17:54:27, Martijn Zwijnenburg wrote: > Hi, > > When we're performing oniom calcs, using G98, the calculation always > crashes due to the fact that in the high-level part of the calculation > the multiplicity doesn't equal the input value of 1. Looking at the > output it seems that gaussian98 doesn't add the necessary terminating > hydrogens. > > Example we did a calculation on trifluoromethylsilane (CH3F3Si) > wherein we treated the trifluoromethyl part on a medium (AM1) level > whereas the rest of molecule was calculated on the High (DFT) level. > > %Chk=oniom_test > #P trackio > # opt ONIOM(B3LYP/sto-3g:AM1) > # NoSymm > > oniom_test job > oniom_test archiving > > 0 1 > SI -0.354 -0.184 0.688 High > C -1.345 -0.451 -0.882 Medium > F -1.135 -1.670 -1.475 Medium > F -2.703 -0.384 -0.701 Medium > F -1.082 0.464 -1.870 Medium > H -0.901 0.971 1.390 High > H 1.037 0.052 0.322 High > H -0.466 -1.381 1.514 High > > The first AM1 calculation gives no problems but before the DFT part of > the oniom calc starts for the first time the programme crashes with > the following error message: > > ONIOM: generating new system at layer 1 > ONIOM: saving gridpoint 3 > ONIOM: restoring gridpoint 9 > Leave Link 120 at Tue Mar 26 12:12:02 2002, MaxMem= 6291456 cpu: 0.0 > (Enter /usr/local/g98/l301.exe) > Standard basis: STO-3G (5D, 7F) > The combination of multiplicity 1 and 17 electrons is impossible. > Error termination via Lnk1e in /usr/local/g98/l301.exe. > Job cpu time: 0 days 0 hours 0 minutes 2.1 seconds. > File lengths (MBytes): RWF= 6 Int= 0 D2E= 0 Chk= 1 Scr= 1 > > The 17 electrons are just the silicon and the three hydrogens. > Apparently the terminating hydrogen is not added by the program. Does > anybody know what is going wrong here and how to fix the problem? Any > suggestions are more then welcome. > > cheers, > > Martijn > > > > ------------------------------------------------------------------------- > Martijn Zwijnenburg Lab. of Applied Organic Chemistry and Catalysis > Delft University of Technology Julianalaan 136 2628 BL Delft The > Netherlands Tel: 0031-(0)152782691 Fax: 0031-(0)152784700 e-mail: > M.A.Zwijnenburg@tnw.tudelft.nl web page: http://come.to/tock > > -= 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 > > > > -- Ataualpa Albert Carmo Braga atabraga@iqm.unicamp.br http://www.iqm.unicamp.br From chemistry-request@server.ccl.net Tue Mar 26 17:52:09 2002 Received: from uranium.camsoft.com ([198.112.109.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QMq9p16758 for ; Tue, 26 Mar 2002 17:52:09 -0500 Received: from potassium (172.17.3.55) by uranium.camsoft.com (Worldmail 1.3.167); 26 Mar 2002 17:52:02 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 26 Mar 2002 17:52:02 -0500 From: "Support" Subject: RE: {Talisma#034-262} Chem 3D Ultra 7.0 as a Gaussian interface. To: "Laurence Lavelle" , "CCL" Message-ID: <2002326_@TLM198535_@TLM> X-Mailer: Talisma Mail Component Version 2.5 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g2QMq9p16759 That's an understandable expectation, but management had a different opinion on how to proceed with the development resources we had available at the time. It was decided to put the resources available on implementing GAMESS and Tinker interfaces. New development resources have become available, but it is still unclear as to when the issues you have reported will be addressed. We do hope to address them in a future release. Regards, Rich Talbot Director, Technical Support CambridgeSoft support@cambridgesoft.com Do you want to know when software patches are available, the latest product problems and solutions, facts, tricks and tips, tidbits and more? Then sign up for our FREE technical support newsletter at: http://www.cambridgesoft.com/support/nl/new.cfm >-----Original Message----- >From: Laurence Lavelle[lavelle@mbi.ucla.edu] >Date: Tuesday, March 26, 2002 01:09 PM >To: Support[support@cambridgesoft.com]; CCL[chemistry@ccl.net] >Subject: Chem 3D Ultra 7.0 as a Gaussian interface. > > >Rich, > >Thank for your prompt and straight forward reply. However I am surprised > >that bugs leading to incorrect bond lengths when using Chem 3D as a >Gaussian interface was not given higher priority three years and two >versions ago. > >I look forward to using version 8. > >Sincerely, >Laurence Lavelle > > > >At 08:52 AM 3/22/2002 -0500, Support wrote: >>Just looking back at our correspondence with you, I have found that the > >>three bugs you have reported and other suggestions have not been >addressed >>in 7.0. The main things that have been added to Chem3D since 5.0 are a > >>GAMESS interface and Tinker. Some bugs have been fixed, too. R&D is >>aware of the items you have reported and we hope to address them in a >>future version, but it is not clear when that will be. >> >>Regards, >> >>Rich Talbot >>Director, Technical Support >>CambridgeSoft >>support@cambridgesoft.com >> >> >>Do you want to know when software patches are available, the latest >>product problems and solutions, facts, tricks and tips, tidbits and >>more? Then sign up for our FREE technical support newsletter at: >>http://www.cambridgesoft.com/support/nl/new.cfm >> >> >> >> >-----Original Message----- >> >From: Laurence Lavelle[lavelle@mbi.ucla.edu] >> >Date: Thursday, March 21, 2002 06:54 PM >> >To: CCL[chemistry@ccl.net] >> >Subject: Chem 3D Ultra 7.0 as a Gaussian interface. >> > >> > >> >I tried using Chem 3D version 5 as a Gaussian interface some time >back >> >but >> >it was full of bugs. >> > >> >Anyone having successful use of Chem 3D Ultra 7.0 as a Gaussian >> >interface ? >> >In particular for pdb files ? >> > >> >Thanks, >> >Laurence >> > >> > >> > > > > From chemistry-request@server.ccl.net Tue Mar 26 18:05:51 2002 Received: from polaris.scs.uiuc.edu ([130.126.225.41]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QN5pp17542 for ; Tue, 26 Mar 2002 18:05:51 -0500 Received: from leonidas (leonidas.scs.uiuc.edu [130.126.226.239]) by polaris.scs.uiuc.edu (8.11.1/8.11.1) with SMTP id g2QN5jA255219 for ; Tue, 26 Mar 2002 17:05:45 -0600 (CST) Reply-To: From: "Jerome Baudry" To: Subject: charmm parameters for Fe3+ heme? Date: Tue, 26 Mar 2002 17:08:01 -0600 Message-ID: <001801c1d51b$14b67660$efe27e82@leonidas> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Importance: Normal Dear All Can anybody point me to parameters for Ferric (Fe3+) heme for use with CHARMM? Thanks a lot, Jerome ---------------------------------------------------------- Jerome Baudry, Ph.D. Computational Research Scientist, Research Coordinator 150 Noyes Lab. Computer Applications & Network Services School of Chemical Sciences University of Illinois at Urbana-Champaign 505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3210; E-mail: jerome@scs.uiuc.edu From chemistry-request@server.ccl.net Tue Mar 26 18:25:41 2002 Received: from dylan.cse.nd.edu ([129.74.32.170]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g2QNPfp18466 for ; Tue, 26 Mar 2002 18:25:41 -0500 Received: from localhost (ako@localhost) by dylan.cse.nd.edu (8.10.2/8.10.2) with ESMTP id g2QNPUe16128 for ; Tue, 26 Mar 2002 18:25:30 -0500 (EST) Date: Tue, 26 Mar 2002 18:25:30 -0500 (EST) From: Alice NgarKit Ko To: Computational Chemistry List Subject: CHARMM RESID error In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I am new to using CHARMM. I made a water box and tried to combine the waterbox pdb file with my protein pdb file using CHARMM and generate the final psf file. But I got the following error: ** ERROR IN SEQRDR ** REPEATED RESID FOR 391 1391 100 when it tried to read the sequence for my waterbox. The RESID for my water box starts from 1 and with a segment ID WATR. There is no water molecules in my protein pdb file. CHARMM read in my protein pdb file without a problem. Only when it got to reading the water box. I don't know why it says I have repeated RESID. Any suggestion will be helpful. Thanks Alice