From chemistry-request@server.ccl.net Tue Jun 18 02:56:24 2002 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5I6uNH17655 for ; Tue, 18 Jun 2002 02:56:23 -0400 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KJ2JHOI0808Y8JKI@Roche.COM> for chemistry@ccl.net; Tue, 18 Jun 2002 08:53:15 +0200 Received: from rbamsemcn1.emea.roche.com (rbamsemcn1.emea.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KJ2JH8LP7W8Y8FL3@Roche.COM>; Tue, 18 Jun 2002 08:52:53 +0200 Received: from rbamsem2.emea.roche.com ([145.245.211.136]) by rbamsemcn1.emea.roche.com with Microsoft SMTPSVC(5.0.2195.2966); Tue, 18 Jun 2002 08:52:51 +0200 Date: Tue, 18 Jun 2002 08:52:51 +0200 From: "Borosy, Andras {Basi~Basel}" Subject: RE: conversion of a 3d image of a molecule to 2d To: Rajarshi Guha , CCL Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft Exchange V6.0.5762.3 Content-type: text/plain; charset=iso-8859-1 Thread-Topic: conversion of a 3d image of a molecule to 2d Thread-Index: AcIWaiuUI53x5IT9QTSyaImKVSrmEQAKjYPA content-class: urn:content-classes:message X-MS-Has-Attach: X-MS-TNEF-Correlator: X-OriginalArrivalTime: 18 Jun 2002 06:52:51.0886 (UTC) FILETIME=[C3FC54E0:01C21694] Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g5I6uOH17656 Cactus tools of TORVS: http://www2.chemie.uni-erlangen.de/software/cactvs/index.html Best wishes, András Borosy Ph.D. computational chemist Project leader Discovery Informatics Basilea Pharmaceutica Ltd POB 3255, 65/316B 4002 Basel Switzerland tel: +41-61-6885469 fax: +41-61-6882139 e-mail: andras.borosy@basileapharma.com www.basileapharma.com > -----Original Message----- > From: Rajarshi Guha [mailto:rajarshi@presidency.com] > Sent: 2002. június 17. 22:11 > To: CCL > Subject: CCL:conversion of a 3d image of a molecule to 2d > > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi, > does anybody know of any freeware programs that will > convert a 3d molecular > structure (from a hin or MDL mol file) to a 2D represenation > suitable for > printing/saving as a gif et al? > > TIA, > > - -- > - ------------------------------------------------------------------- > Rajarshi Guha | email: rajarshi@presidency.com > 417 Davey Laboratory | web : http:// www.jijo.cjb.net > Dept. Of Chemistry | ICQ : 123242928 > Pennsylvania State University | AIM : LoverOfPanda > - ------------------------------------------------------------------- > GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A > Public Key : http://pgp.mit.edu/ > - ------------------------------------------------------------------- > Breadth-first search is the bulldozer of science. > -- Randy Goebel > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.0.6 (GNU/Linux) > Comment: For info see http://www.gnupg.org > > iD8DBQE9DkJgzcRVdJAXryoRAv4cAJkBVVvyfqtbSfqERGZeAu6svSAfXgCggydc > TFladPuZ6Y7O3gULK6gkBZE= > =N517 > -----END PGP SIGNATURE----- > > > > -= 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 Tue Jun 18 10:04:15 2002 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5IE4Fn23767 for ; Tue, 18 Jun 2002 10:04:15 -0400 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id KAA23106; Tue, 18 Jun 2002 10:04:15 -0400 (EDT) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Tue, 18 Jun 2002 10:02:20 -0400 Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0GXW00DP1MT199@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Tue, 18 Jun 2002 09:58:13 -0400 (EDT) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Tue, 18 Jun 2002 10:01:41 -0400 Content-return: allowed Date: Tue, 18 Jun 2002 10:01:32 -0400 From: "Shobe, Dave" Subject: CI, CC, and CAS To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629D01C15DC1@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 I would like to learn more about the various multi-determinant methods used for electron correlation. I'd like something more substantial than the Foresman and Frisch book, but I'm not ready to read the J. Chem. Phys. articles yet. They seem to dive immediately into unfamiliar symbols. I'm not sure if what I need is a "refresher course" in quantum mechanics, or if there are some standard symbols that quantum-chemical method developers use among themselves that they don't feel a need to define them (sort of like using S for entropy). Perhaps a "historical approach" where I start with the earliest-developed methods would help me with that? If anyone has advice on this, even if it's "NO!! Don't do it, if you value your sanity!" :-), I'd like to have it. --David Shobe From chemistry-request@server.ccl.net Tue Jun 18 10:05:18 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g5IE5IO23804 for chemistry; Tue, 18 Jun 2002 10:05:18 -0400 Message-ID: <004001c216df$0b2223a0$fcdcf143@anick000> From: "David J Anick" To: "Jan Labanowski" References: Subject: Summary: Thermal corrections at T .ne. 298 K Date: Tue, 18 Jun 2002 08:44:32 -0700 To All, Heartfelt thanks to the many of you who responded to my query regarding computation of thermal corrections at temperatures other than 298 K. The original query is repeated here, followed by summary of responses. While all responses are useful, Karl Irikura's perl script was the quickest and easiest way to solve my problem, and I recommend it to anyone else faced with the same situation. David Anick David.Anick@gte.net ======================================== Dear CCLers, Having completed a Gaussian98 frequencies/ZPE calculation at an optimized geometry, I now find that I would like to know the thermal corrections to energy, enthalpy and Gibbs free energy at a different temperature (77 K) than the one that Gaussian98 automatically calculated (298 K). I don't want to re-run the calculation if possible because it took nearly a week. Can anyone tell me the formula(s) that Gaussian98 uses to compute these data? If it involves integrating Cp or Cp/T, how do I obtain Cp as a function of temperature? Thank you in advance, David Anick MD PhD David.Anick@gte.net ======================================== From: "Huajun Fan" Hi, Actually, to obtain the therm values at different temperature is fairly fast and easy once you had the 298K one. Here is an example of input: ---beginning of file-- %Chk=yourcheckfilename.chk # b3lyp/yourbasisset pseudo=read freq(readiso readfc) geom=allcheck 523.15 1.0 ECP goes here --end of file-- this calculation on this kind should take less than a minute. Hope this helps. huajun ------------------------------------------------------------- From: "Stefan Fau" Hi David, if you still have the checkpoint-file of the frequency calculation, you can reuse the force constants in there. I forgot the details, but I dimly remember a keyword like # ... freq(readisotope) It calculates thermodynamic data with non-standard settings and can use data > from the checkpoint-file. Stefan ------------------------------------------------------------- From: "Karl Irikura" Hi. I have a Perl script that will compute S, Cp, and H(T)-H(0) from a G98 frequency output file. I'll send it to you if you like. I can also send a reprint of a book appendix that shows all the equations. Best wishes, Karl I. Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura@nist.gov http://www.nist.gov/compchem/ ------------------------------------------------------------- From: "Dinamica" You can re-run G98 to recompute the vibrational analysis & thermodynamics in the conditions you ainterested by using formchk. And also the g98 w/ some read= option (sorry i do not remeber it now.) You should check a Gaussian white-paper on their www which describes how they obtain thermochemiscal data from frequencies. hope to have helped, greetings, Guilherme ------------------------------------------------------------- From: "Wai-To Chan" There is a paper "Thermochemistry in Gaussian" by Joseph W. Ochterski at Gaussian Inc which may be helpful. The paper is probably still available from the gaussian homepage. I suppose you didn't save the checkpoint file. There is this utility program freqchk which I've never used in the g98 package that may do what you want if you have the check file. I have a simple fortran code that can restore thermochemical quantities including H and G from a g98 frequency output file (default printing option required) at specified temperature. A while ago I posted the code in response to a similar question. Email me if you need it and I will repost it. Wai-To Chan ------------------------------------------------------------- From: "Dave Harris" If you still have either a checkpoint (.chk) file or a formatted checkpoint (.fchk) file produced by the original frequency calculation, you can use the freqchk utility to calculate thermodynamic parameters for different temperatures, pressures, and isotope masses. It can also be used to change the scaling factor applied to calculated vibrational frequencies. Info from Gaussian is at: > Can anyone tell me the formula(s) that Gaussian98 uses > to compute these data? This can also be found at the Gaussian site: Regards, -- Dave Harris Department of Chemistry University of Missouri-Kansas City ------------------------------------------------------------- From: "Steve Williams" If you still have the checkpoint file there is a g98 utility program (freqcheck?) that will do exactly what you want. If not you can compute the corrections yourself from the freq's you have in the g98 output file. Look in any pchem textbook for the formulae for rot, trans, and vib contributions to energy of ideal gas; these will be in the chapter on simple statistical mechanics. ------------------------------------------------------------- From: "Laurence Cuffe" There's a couple of good papers on the gaussian web site, however if you have the checkpoint file from the completed job then the freqchk utility may be useful it "may be used for retrieving frequency and thermochemistry data > from a checkpoint file with optional specification of an alternate temperature, pressure, scale factor, and or isotope substitution" I've used it and found it straightforward and stable in operation. All the best Laurence Cuffe ------------------------------------------------------------- From: "Viswanathan Balakrishnan" Sir, If you have saved the check file, then you can use the Gaussian utility Freqchk and change the temperature. I usually perform these calculations as an additional step in the main job using the keyword freq(readisotopes). The first line required (after the molecular specification) contains the temperature (Kelvin) followed by pressure (bar) separated by a space. If you want to make isotopic substitutions, they are described in the following lines. Hope this is of some help. Balakrishnan Balakrishnan Viswanathan ------------------------------------------------------------- From: "Shobe, Dave" Try this: #n [theory level here] freq=(readfc,readiso) geom=check guess=read Where the Z-matrix would go, put a blank line and then a line with the new temperature and pressure (as floating point numbers). This is VERY fast! --David From chemistry-request@server.ccl.net Tue Jun 18 11:21:07 2002 Received: from kafka.net.nih.gov ([165.112.130.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5IFL7n25865 for ; Tue, 18 Jun 2002 11:21:07 -0400 Received: from I.T.S.ME ([129.43.27.170]) by kafka.net.nih.gov (/8.10.1) with ESMTP id g5IFL7Q07693; Tue, 18 Jun 2002 11:21:07 -0400 (EDT) Date: Tue, 18 Jun 2002 11:19:31 -0400 (Eastern Daylight Time) From: "M. Nicklaus" To: CCL cc: Rajarshi Guha , mn1@helix.nih.gov Subject: Re: CCL:conversion of a 3d image of a molecule to 2d In-Reply-To: Message-ID: X-X-Sender: mn1@helix.nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 18 Jun 2002, Borosy, Andras {Basi~Basel} wrote: > Cactus tools of TORVS: > > http://www2.chemie.uni-erlangen.de/software/cactvs/index.html ...and the CACTVS-based online tools, available at http://www2.chemie.uni-erlangen.de/services/gifcreator/index.html http://cactus.nci.nih.gov/services/gifcreator/ Marc ------------------------------------------------------------------------ Marc C. Nicklaus, Ph.D. NIH/NCI at Frederick E-mail: mn1@helix.nih.gov Bldg 376, Rm 207 Phone: (301) 846-5903 376 Boyles Street Fax: (301) 846-6033 FREDERICK, MD 21702 USA Head, Computer-Aided Drug Design MiniCore Facility Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute at Frederick, National Institutes of Health http://rex.nci.nih.gov/RESEARCH/basic/medchem/mcnbio.htm ------------------------------------------------------------------------ From chemistry-request@server.ccl.net Tue Jun 18 13:10:39 2002 Received: from gil.axelero.hu ([195.228.240.76]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5IHAcn28007 for ; Tue, 18 Jun 2002 13:10:38 -0400 Received: from chemaxon.com (user164.obuda.axelero.hu [195.228.88.164]) by mail01.axelero.hu (iPlanet Messaging Server 5.1 HotFix 0.9 (built May 30 2002)) with ESMTP id <0GXW0073JVPOH5@mail01.axelero.hu> for chemistry@ccl.net; Tue, 18 Jun 2002 19:10:36 +0200 (MEST) Date: Tue, 18 Jun 2002 19:10:31 +0200 From: Ferenc Csizmadia Subject: Re: CCL:conversion of a 3d image of a molecule to 2d To: CCL Message-id: <3D0F6987.7070401@chemaxon.com> Organization: ChemAxon MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7BIT X-Accept-Language: en-us, hu User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.0.0) Gecko/20020530 References: <200206171611.12570.rajarshi@presidency.com> Rajarshi Guha wrote: > does anybody know of any freeware programs that will convert a 3d molecular >structure (from a hin or MDL mol file) to a 2D represenation suitable for >printing/saving as a gif et al? > You can use the MolConverter application available in the Marvin Beans package. It can generate images (PNG, JPG, SVG, ...) or other file formats. User's guide: http://www.chemaxon.com/marvin/doc/molconvert.html. Using MolConverter is free for academic or home users. (The MarvinSketch and MarvinView applications also.) The software is in Java, so you can run it in practically any operating system. You can download Marvin Beans at http://www.chemaxon.com/products.html Best regards, Ferenc From chemistry-request@server.ccl.net Tue Jun 18 15:23:59 2002 Received: from pony.its.uwo.ca ([129.100.2.63]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5IJNwn30171 for ; Tue, 18 Jun 2002 15:23:59 -0400 Received: from femail.its.uwo.ca (hurdle.its.uwo.ca [129.100.2.108]) by pony.its.uwo.ca (8.12.1/8.12.0) with ESMTP id g5IJNuiR018968 for ; Tue, 18 Jun 2002 15:23:57 -0400 (EDT) Received: from woolabpcvsj70k (woolabpc3.chem.uwo.ca [129.100.61.41]) by femail.its.uwo.ca (8.12.1/8.12.0) with SMTP id g5IJNkFq020668 for ; Tue, 18 Jun 2002 15:23:47 -0400 (EDT) Message-ID: <016701c216fd$98340c40$293d6481@woolabpcvsj70k> From: "sdecker" To: Subject: Calculating Stress Tensor in CPMD simulations Date: Tue, 18 Jun 2002 15:23:14 -0400 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0164_01C216DC.10CCD230" 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 This is a multi-part message in MIME format. ------=_NextPart_000_0164_01C216DC.10CCD230 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi All, I am relatively new to the field of Car-Parrinello Molecular = Dynamics and the commonly employed programs to do these simulations and = I was hoping that someone in the CCL will be able to help me with a = problem I have encountered. In particular, I am having problems = calculating the stress tensor (to obtain the hydrostatic pressure) = during an NVE simulation of a liquid with the program CPMD. I am able = to calculate the stress tensor for a test system of liquid H2O with 32 = molecules in the simulation cell with CPMD versions 3.4.3 and 3.5.1. = However, when I try to calculate the stress tensor for my system of = interest: liquid nitromethane (CH3NO2) with 32 molecules in the = simulation cell I cannot do so. With CPMD version 3.4.3 my job exits = with an error stating that more programming is required, and with CPMD = version 3.5.1 my job becomes frozen during the initialization right = after generating the atomic basis set and just before it goes through = some sort of initialization routine for the stress tensor. Has anyone = encountered a similar problem. Since I am able to calculate the stress = tensor for the smaller liquid H2O system it seems like this may be due = to a restriction on the system size. Does anyone know if this is indeed = the case? =20 Your help would be greatly appreciated. Sincerely, Stephen Decker _________________________________________________ Dr. Stephen A. Decker, Ph.D. NSERC Postdoctoral Fellow Department of Chemistry =20 University of Western Ontario London, Ontario, Canada N6A 5B7 phone: (519)-661-2111 ext. 86353 =20 fax: (519)-661-3022 email: sdecker@uwo.ca _________________________________________________ ------=_NextPart_000_0164_01C216DC.10CCD230 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi All,
 
    I am relatively new = to the field=20 of Car-Parrinello Molecular Dynamics and the commonly employed programs = to do=20 these simulations and I was hoping that someone in the CCL = will be=20 able to help me with a problem I have = encountered.  In particular, I am having problems calculating = the stress=20 tensor (to obtain the hydrostatic pressure) during an NVE = simulation of a=20 liquid with the program CPMD.  I am able to calculate the stress = tensor for=20 a test system of liquid H2O with 32 molecules in the simulation = cell with=20 CPMD versions 3.4.3 and 3.5.1.  However, when I try=20 to calculate the stress tensor for my system of interest: liquid=20 nitromethane (CH3NO2) with 32 molecules in the simulation cell I = cannot do=20 so.  With CPMD version 3.4.3 my job exits with an error = stating=20 that more programming is required, and with CPMD version 3.5.1 my = job=20 becomes frozen during the initialization right after generating the = atomic=20 basis set and just before it goes through some sort of = initialization=20 routine for the stress tensor.  Has anyone encountered a = similar=20 problem.  Since I am able to calculate the stress tensor for = the=20 smaller liquid H2O system it = seems like this=20 may be due to a restriction on the system size.  Does anyone = know if=20 this is indeed the case?   
 
    Your help would = be greatly=20 appreciated.
 
    = Sincerely,
 
    Stephen Decker
 
_________________________________________________
 
 Dr. Stephen A. Decker, = Ph.D.
 NSERC=20 Postdoctoral Fellow
 
 Department of Chemistry =20
 University of Western Ontario
 London, Ontario, =20 Canada
 N6A 5B7
 
 phone: (519)-661-2111 ext.=20 86353         =20
 fax:     =20 (519)-661-3022
 email:  sdecker@uwo.ca
____________________= _____________________________
------=_NextPart_000_0164_01C216DC.10CCD230-- From chemistry-request@server.ccl.net Tue Jun 18 14:03:08 2002 Received: from mallard.duc.auburn.edu ([131.204.2.23]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5II38n28659 for ; Tue, 18 Jun 2002 14:03:08 -0400 Received: from localhost (kwonohy@localhost) by mallard.duc.auburn.edu (8.9.3/8.9.3) with SMTP id NAA21943 for ; Tue, 18 Jun 2002 13:03:08 -0500 (CDT) X-Authentication-Warning: mallard.duc.auburn.edu: kwonohy owned process doing -bs Date: Tue, 18 Jun 2002 13:03:07 -0500 (CDT) From: Ohyun Kwon X-Sender: kwonohy@mallard To: chemistry@ccl.net Subject: basis set for Zn Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Cclers; Could anybody recommend me some basis sets for Zn (either ECPs or full electron basis sets)? Thank you very much in advance. Best wishes, Tommy Kwon, Ph.D email : kwonohy@mail.auburn.edu homepage : http://www.auburn.edu/~kwonohy From chemistry-request@server.ccl.net Tue Jun 18 18:17:45 2002 Received: from toni.schrodinger.com ([192.156.98.56]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g5IMHin01201 for ; Tue, 18 Jun 2002 18:17:44 -0400 Received: (from announce@localhost) by toni.schrodinger.com (8.8.8/8.8.5) id PAA22500 for chemistry@ccl.net; Tue, 18 Jun 2002 15:17:39 -0700 Message-Id: <200206182217.PAA22500@toni.schrodinger.com> Subject: Molecular modeling just got better with MacroModel 8.0 To: chemistry@ccl.net Date: Tue, 18 Jun 2002 15:17:39 -0700 (PDT) From: Schrodinger Announce Account Reply-To: Schrodinger Information Account X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger is pleased to announce the release of MacroModel 8.0, the latest version of our popular molecular-modeling software. MacroModel has a large selection of force fields, as well as advanced methods for conformational analysis, molecular dynamics, and free energy calculations, making it the gold standard for general-purpose molecular mechanics studies of organic and bioorganic molecules in gas phase or solution. Powerful new utilities extend MacroModel for exploration of proteins and protein-ligand complexes. New features in MacroModel 8.0 include: * a unique algorithm which performs conformational searches on protein-sized structures; applications include generation of alternate protein structures for docking studies and study of a protein's response to new ligands, * bond-dipole cutoffs for significantly more accurate electrostatic potential energy, * eMBrAcE, an easy to use tool for multiple minimization of docked ligands, * an advanced symmetry recognition algorithm, which quickly compares and eliminates duplicate structures in conformational analysis, * protein loop structure generation, which performs conformational searches on a series of residues in a protein; alternate residue sequences can also be specified. MacroModel 8.0 ships with Maestro 5.0, the latest version of our graphical user interface. Highlights of Maestro 5.0 include: * scientific visualization of van der Waals and other molecular surfaces, * mapping of hydrophilic and hydrophobic regions in protein active sites, * interactive property plots (scatter or frequency), where one can select molecules for further analysis by selecting points in the graph. For more information about obtaining MacroModel 8.0, please contact your client representative or visit http://www.schrodinger.com. From chemistry-request@server.ccl.net Tue Jun 18 20:48:39 2002 Received: (from ccl@localhost) by server.ccl.net (8.11.6/8.11.0) id g5J0mdL13941 for chemistry; Tue, 18 Jun 2002 20:48:39 -0400 From: "Prof. Chan Kyung Kim" To: jkl@ccl.net Message-ID: <002001c21436$615f24d0$619af6a5@TEST> Subject: How to calculate surface area and volume of the isodensity surface? Date: Sat, 15 Jun 2002 15:32:08 +0900 Dear Computational Chemists: Using Gaussian 98 and Molden, I can generate (x,y,z) coordinates of a molecular surface with isodensity level 0.001. Using this coordinates, I want to calculate molecular surface area(and volume). Is there any program which can do that? I found two programs from CCL archive. But these programs calculate molecular surface/volume based on atomic coordinate not (x,y,z) coordinates of molecular surface. Thank you in advance. Chan Prof. Chan Kyung Kim Department of Chemistry Inha University Inchon, 402-751, Korea (Tel) +82-32-860-7684 (Fax) +82-32-867-5604 (email) kckyung@inha.ac.kr