From chemistry-request@server.ccl.net Thu Dec 12 03:21:51 2002 Received: from oc30.uni-paderborn.de ([131.234.240.90]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBC8Lpi22113 for ; Thu, 12 Dec 2002 03:21:51 -0500 Received: (from ib@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) id LAA71913; Wed, 11 Dec 2002 11:32:32 +0100 (CET) Date: Wed, 11 Dec 2002 11:32:32 +0100 (CET) Message-Id: <200212111032.LAA71913@oc30.uni-paderborn.de> X-Authentication-Warning: oc30.uni-paderborn.de: ib set sender to ib@oc30.uni-paderborn.de using -f From: Ingo Brunberg To: rajarshi@presidency.com CC: chemistry@ccl.net In-reply-to: <200212111444.24969.rajarshi@presidency.com> (message from Rajarshi Guha on Wed, 11 Dec 2002 14:44:20 -0500) Subject: Re: CCL:plotting molecular surfaces References: <200212111444.24969.rajarshi@presidency.com> > Hi, > I have used Molekel for plotting surfaces made of electrostatic potentials. > I'd like to do this for a similar problem - rather than atomic charges, I > want to plot atomic hydrophobicities. I have a program which reads Hyperchem > HIN files and caluclates the hydrophobicity values. The resultant output > consists of atom type, value. I also have at hand the x,y,z coordinates of > the atoms (from the hin file). > > Essentially this is analogous to plotting an electrostatic potential surface - > Molekel reads in Gaussian cube format. Thus if I could put my data in this > format Molekel should be able to do the job. > > Is the format spec available anywhere? The gaussian cube format is described in the gaussian manual. Even with little programming experience it should be relatively straigthforward to write your own format converter. > > But apart from the Molekel route does anybody have any pointers as to how I > could go about visualizing my data using freely available code. If you have the cube files you could also try gOpenMol. Regards, Ingo Brunberg > > Thanks, > > - -- > - ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > - ------------------------------------------------------------------- > Alcohol, an alternative to your self > - 'Alcohol' by the Bare Naked Ladies From chemistry-request@server.ccl.net Thu Dec 12 11:16:10 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBCGG9i10131 for ; Thu, 12 Dec 2002 11:16:09 -0500 Received: from fy.chalmers.se (ftf-pc24.fy.chalmers.se [129.16.112.154]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id RAA15118 for ; Thu, 12 Dec 2002 17:14:56 +0100 (MET) Message-ID: <3DF8B642.3050001@fy.chalmers.se> Date: Thu, 12 Dec 2002 17:16:02 +0100 From: Henrik Nilsson User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.1) Gecko/20020823 Netscape/7.0 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: HF/Sadlej calculations Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All Has anyone experienced redicolous values of the mulliken charges calculated by ab initio quantum mechanical methods with HF/Sadlej-pvz basis set? Here is an example and corresponding data calculated with HF/6-31G*. The Lowdin charges are similar but the mulliken are totally off. The calculations of Raman intensities also gave "slightly" high values ~19000 A**4/AMU for a CN-vibration. Regards, Henrik From chemistry-request@server.ccl.net Thu Dec 12 11:05:59 2002 Received: from compchem.dfh.dk ([130.225.225.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBCG5wi09759 for ; Thu, 12 Dec 2002 11:05:59 -0500 Received: (from jeremy@localhost) by compchem.dfh.dk (SGI-8.9.3/8.9.3) id QAA23126 for chemistry@ccl.net; Thu, 12 Dec 2002 16:54:54 +0100 (MET) Date: Thu, 12 Dec 2002 16:54:54 +0100 From: "Jeremy R. Greenwood" To: chemistry@ccl.net Subject: Summary: two visualisation questions Message-ID: <20021212165453.A1221414@compchem.dfh.dk> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Hi CCList, Summary of responses to Subject: CCL:Two visualisation questions Date: Fri, 6 Dec 2002 17:49:15 +0100 ---------------------------------------------------------------------- My first question concerned software for visualising molecular data P(X,Y,Z) calculated at a set of abitrary (non-grid) points. Thanks to Jim Kress who listed: gOpenMol (http://www.csc.fi/gopenmol/), Molden (http://www.caos.kun.nl/~schaft/molden/molden.html), GaussView (www.gaussian.com), Molekel (http://www.cscs.ch/molekel/) Of these, gOpenMol seems to be the most flexible/powerful, but it seems it would still require me to order and interpolate my data onto a cubical grid in .plt format. Thanks to Carsten Menke at Accelrys, who pointed out that Materials Studio can visualise the .grd format, which though still a grid, need not be cubic: Accelrys software can also handle arbitrary rhombic grids (e.g. from solid phase unit cell). Many thanks to Aldo Jongejan who put me onto Dino: http://cobra.mih.unibas.ch/dino -- this nifty program is still intended for chemists (emphasis on large molecules) yet it can handle a very wide variety of data and rendering. The install was also trivial, and the hardware stereo works straight out. I'll be using it first. Thanks to Fred P. Arnold and Malcolm Gillies who recommended OpenDX. http://www.opendx.org -- this is an advanced, general visualisation suite, and is no doubt the most powerful suggestion, offering spectacular rendering of multidimensional data sets. It's not specifically for chemists though, and may have a steeper learning curve than the above. I also found that it is not trivial at present to get it working under IRIX; there are compiler, library, and supporting software version issues. Other platforms are probably better supported though, and it seems to be under quite rapid development. ---------------------------------------------------------------------- My second request was for a handy tool for processing QM spectral predictions into convincing curves to show to spectroscopists. Thanks to E. Lewars who gave me references to the use of both Gaussian and Lorentzian functions in IR: H. Lampert et. al., J. Phys. Chem. A, 1997, 101, 2254-2263. (Gaussians) M. D. Haus, H. B. Schlegel, J. Chem. Phys, 1998, 109, 10587-10593. (Lorentzians) Lorentzians are also used in VCD: F.J. Devlin et al., J. Phys. Chem. A., 1997, 101, 6322-6333 Thanks again to Aldo Jongejan who pointed out Paul D. Soper's spectrum.c in the CCL archives: http://server.ccl.net/cca/software/SOURCES/C/IR-spectrum/README.shtml -- in conjunction with a little scripting and some plotting software, this little program does the job, not only for IR, but pretty much any spectroscopic data from QM, including signed spectra such as ECD and VCD. E. Lewars requests (and so do I) feedback on which curve shape (Gaussian or Lorentzian) better reproduces experimental spectra for various kinds of spectroscopy (e.g. IR, NMR, UV/Vis, VCD, ECD). --Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy@greenwood.net Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Dec 12 11:00:30 2002 Received: from MAIL.AD.Berry.edu ([66.20.28.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBCG0Ui09597 for ; Thu, 12 Dec 2002 11:00:30 -0500 Received: from [10.16.232.24] ([10.16.232.24]) by MAIL.AD.Berry.edu with Microsoft SMTPSVC(5.0.2195.5329); Thu, 12 Dec 2002 10:55:50 -0500 User-Agent: Microsoft-Outlook-Express-Macintosh-Edition/5.02.2022 Date: Thu, 12 Dec 2002 11:00:26 -0500 Subject: TS calculation From: Gary Breton To: Message-ID: Mime-version: 1.0 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-OriginalArrivalTime: 12 Dec 2002 15:55:50.0586 (UTC) FILETIME=[F18531A0:01C2A1F6] Hello everyone, I have been running some TS calculations on the decompositions of diazetines, which are four-membered ring azo compounds. Diazetines eliminate N2 to give alkenes at elevated temperatures. A paper was recently published (Yamabe, S.; Minato, T. J. Chem. Phys. A 2001, 7281) that determined the geometry of the TS for the unsubstituted case (i.e., C2H4N2). They reported that due to the high biradical character of the TS, HF and DFT methods failed. The completely active space method (CASSCF(2,2)) was found to work well. I similarly found that HF and DFT methods failed to locate a TS, but CASSCF(2,2) located the TS efficiently. I am interested in the decomposition of a series of derivatives of this diazetine (i.e., with substitution). I made a guess at the TS for the substituted derivatives using the TS geometry of the unsubstituted diazetine, and ran the following calculation in Gaussian: # casscf(2,2)/6-31g(d) opt=(ts,calcFC,noeigentest) Freq On two derivatives this worked very well. I obtained a TS with a single negative frequency, and when animated it followed the expected pathway. On the third (and crucial one of course) the calculation failed with the following error: CALCULATION TERMINATED ATTEMPT TO DO ORBITAL ROTATION GREATER THAN 45 DEGREES YOU HAVE CHOSEN THE WRONG STARTING ORBITALS ********** Error termination via Lnk1e in C:\G98W\l510.exe. Job cpu time: 0 days 9 hours 46 minutes 24.0 seconds. File lengths (MBytes): RWF= 903 Int= 0 D2E= 0 Chk= 4 Scr= 1 Gaussian was nice enough to tell me I chose the wrong starting orbitals, but exactly where should I proceed from here. Also, all of these derivatives are very close to each other in structure (the failed compound is simply a saturated derivative of another that worked fine, and the C=C double bond is remote from the reaction site) and it surprises me that two work well and the other experiences this problem. Any sage words of advice would be appreciated. Gary W. Breton Chair and Associate Professor Department of Chemistry Berry College PO Box 495016 Mount Berry, GA 30149 "There's a light at the end of the tunnel, but it may be an oncoming train" From chemistry-request@server.ccl.net Thu Dec 12 16:51:51 2002 Received: from compton.acpub.duke.edu ([152.3.233.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gBCLpoi16806 for ; Thu, 12 Dec 2002 16:51:50 -0500 Received: from CONCORDIA (concordia.lib.duke.edu [152.16.191.233]) by compton.acpub.duke.edu (8.12.4/8.12.4/Duke-5.0.0) with SMTP id gBCLpeO3008717; Thu, 12 Dec 2002 16:51:45 -0500 (EST) X-Originating-IP: 152.3.169.5 X-Mailer: MyDuke.com X-Originator-Info: jz7@acpub From: To: Subject: add hydrogen Date: Thu, 12 Dec 2002 16:46:55 -0500 Message-ID: <004501c2a227$fd53b160$eabf1098@CONCORDIA> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit Thread-Index: AcKiJ/1RVkeJZGeQQ0SCgl8N89Fc4A== Content-Class: urn:content-classes:message X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Dear all, I was trying to use UHBD to calculate the electrostatic potential of a protein-DNA complex. But all the atoms miss hydrogen, which makes the calculation quite wrong. Our group don't have Charmm (and Amber? maybe don't have it). Is there a good way to add all those missing hydrogens? I'm using OPLS parameter for protein and DNA. Another quick question is what is the naming of DNA bases in Amber? Thanks in advance! From chemistry-request@server.ccl.net Thu Dec 12 13:30:42 2002 Received: from web80301.mail.yahoo.com ([66.218.79.17]) by server.ccl.net (8.11.6/8.11.0) with SMTP id gBCIUgi13197 for ; Thu, 12 Dec 2002 13:30:42 -0500 Message-ID: <20021212183033.56193.qmail@web80301.mail.yahoo.com> Received: from [207.225.232.131] by web80301.mail.yahoo.com via HTTP; Thu, 12 Dec 2002 10:30:33 PST Date: Thu, 12 Dec 2002 10:30:33 -0800 (PST) From: Gustavo Mercier Reply-To: gamercier@yahoo.com Subject: Re: [MMTK] [PyMOL] improving interoperability between python molecule toolkits (fwd) To: pyquante-users@lists.sourceforge.net, pymol-users@lists.sourceforge.net, mmtk@starship.python.net, chemistry@ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-1233729932-1039717833=:53645" --0-1233729932-1039717833=:53645 Content-Type: text/plain; charset=us-ascii Hi! I think the comments below are right on the money. I believe that a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry. For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the "black box". The scripting power of Python together with a set of modules would be the best tool for such a course. The students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects. Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain MMTK, PyQuante, PyMol, etc. may be willing to take the initiative. The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel. As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard". Gustavo Eugen Leitl wrote: -- -- Eugen* Leitl leitl ______________________________________________________________ ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org 83E5CA02: EDE4 7193 0833 A96B 07A7 1A88 AA58 0E89 83E5 CA02 http://moleculardevices.org http://nanomachines.net ---------- Forwarded message ---------- Date: Thu, 12 Dec 2002 16:58:47 +1030 From: Michael Sorich To: pymol-users@lists.sourceforge.net Subject: [PyMOL] improving interoperability between python molecule toolkits Hello all, I share in Warren's vision of extending PyMol into a "complete platform for crystallography, computational chemistry, modeling, and informatics". However, I believe this can only come about by cooperation and integration with other python based molecule toolkits. It seems to be in everyone's interest to allow easy interoperation between the toolkits. However, in my experience it is a frustrating and difficult task, even for relatively simple tasks. Does anyone else feel the same frustration? And if so, does anyone have a solution? I believe that a common set of core modules is required. The most important feature is the molecule. -- Gustavo A. Mercier, Jr., MD,PhD Seattle Nuclear Medicine & U/S Associates 1229 Madison, Suite 1150 Seattle, WA 98104-1377 voice: 206-386-6300; fax: 206-386-6312 gamercier@yahoo.com --------------------------------- Do you Yahoo!? New DSL Internet Access from SBC & Yahoo! --0-1233729932-1039717833=:53645 Content-Type: text/html; charset=us-ascii

Hi!

I think the comments below are right on the money.

I believe that a molecular modeling package powered by Python is a great idea, particularly for those who would like to teach computational chemistry.

For example, many popular modeling packages allow the students to perform simulations using a black box approach. This is fine for introductory courses where the focus is on the end results relevant to the chemistry of a problem. In advanced undergraduate course, an instructor may wish to breakthrough the "black box". The scripting power of Python together with a set of modules would be the best tool for such a course. The students could program simulations using objects available through the modules. Each layer of the black box can be peeled by programming with lower level objects.

Although I've been a bit away from Python (my last heavy use was with version 1.5x!), I certainly will support and even contribute to this effort. Unfortunately, the issue is one of leadership to initiate such a project. May be those who mantain MMTK,  PyQuante, PyMol, etc. may be willing to take the initiative.

The definition of a common object/data structure for the "molecule" is a first step. This is a critical step and a little bit of thought may go along way to make development not only easier but useful. It would be best not to rediscover the wheel.

As a suggestion, let's consider the chemistry implementation of XML -- CML. Whatever the details of the object "molecule", it would be beneficial to input and output to/from CML. A specification of "molecule" based on CML would make it easier to interface with other technologies. I recognize that there are problems with CML, but this should not stop the community from considering this "standard".

Gustavo

 Eugen Leitl <eugen@leitl.org> wrote:



--
-- Eugen* Leitl leitl
______________________________________________________________
ICBMTO: N48 04'14.8'' E11 36'41.2'' http://eugen.leitl.org
83E5CA02: EDE4 7193 0833 A96B 07A7 1A88 AA58 0E89 83E5 CA02
http://moleculardevices.org http://nanomachines.net

---------- Forwarded message ----------
Date: Thu, 12 Dec 2002 16:58:47 +1030
From: Michael Sorich
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] improving interoperability between python molecule toolkits

Hello all,

I share in Warren's vision of extending PyMol into a "complete platform
for crystallography, computational chemistry, modeling, and
informatics". However, I believe this can only come about by cooperation
and integration with other python based molecule toolkits.

<cut stuff ...>

It seems to be in everyone's interest to allow easy interoperation
between the toolkits. However, in my experience it is a frustrating and
difficult task, even for relatively simple tasks.

Does anyone else feel the same frustration? And if so, does anyone have
a solution?

I believe that a common set of core modules is required. The most
important feature is the molecule.

<cut stuff ...>

 



--
Gustavo A. Mercier, Jr., MD,PhD
Seattle Nuclear Medicine & U/S Associates
1229 Madison, Suite 1150
Seattle, WA 98104-1377
voice: 206-386-6300; fax: 206-386-6312
gamercier@yahoo.com 


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