From chemistry-request@www.ccl.net Mon Mar 1 04:15:48 1999 Received: from host23.lctn.u-nancy.fr (host23.lctn.u-nancy.fr [192.54.210.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id EAA10107 Mon, 1 Mar 1999 04:15:47 -0500 (EST) From: assfeld@host23.lctn.u-nancy.fr Received: (from assfeld@localhost) by host23.lctn.u-nancy.fr (AIX4.3/UCB 8.8.8/8.7) id KAA19548; Mon, 1 Mar 1999 10:15:10 +0100 Date: Mon, 1 Mar 1999 10:15:10 +0100 Message-Id: <199903010915.KAA19548@host23.lctn.u-nancy.fr> To: chemistry@www.ccl.net, plin@mail.chem.tamu.edu Subject: Re: CCL:Fixed MOs in SCF calculation Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-MD5: gKwzqkrjmGnj1+c/FglbWA== You wrote : Hello, I wanted to know if it is possible to fix some MOs in SCF calculation, say, I provide the required MO coefficients in the input file, and I want them hold unchanged and get solutions of other MOs. Thanx, P. Lin Dear P. Lin, just have a look at paper : X. ASSFELD, and J.-L. RIVAIL, Chem. Phys. Lett. 263, (1996) 100-106. In this paper paper you will find a general formalism to perform SCF calculations with frozen orbitals. We called this method LSCF for "Local SCF" since only some molecular orbitals are variationnally optimized. These method was thought at first for QM/MM technics on macromolecules but is applicable with no difficulty to any type of molecular spinorbitals (occupied or not!). This is very simple to implement in Gaussian, Gamess,... If you need further informations I will be very glad to help. Sincerely yours. ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.u-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.u-nancy.fr From chemistry-request@www.ccl.net Mon Mar 1 05:03:24 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id FAA10295 Mon, 1 Mar 1999 05:01:47 -0500 (EST) Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id LAA28824 for ; Mon, 1 Mar 1999 11:02:26 +0100 (MET) Date: Mon, 1 Mar 1999 11:01:07 +0100 (MET) From: Pablo Vitoria Garcia To: ccl Subject: Viewmol(2.2 or 2.1.1) on DEC Alpha with Mesa Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi all, I recently dowloaded the program Viewmol (2.2), and compiled and linked it with no strange messages in my Dec Alpha OSF1 with Mesa. But the program does not work due to a "Segmentation Fault". I decided to try the previous version (2.1.1). It runs quite OK (the visualization of the IR/Raman modes is fantastic! I love it!) with Gaussian outputs. But the visualization of orbitals behaves very strangely, it is useless. Did anybody succesfully installed Viewmol 2.2 (or 2.1.1) on a Dec Alpha? Could you give me any hints about which the problem may be? Thanks a lot Pablo -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 -------------------------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 1 05:39:39 1999 Received: from nic.upatras.gr (nic.upatras.gr [150.140.1.30]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id FAA10539 Mon, 1 Mar 1999 05:39:35 -0500 (EST) Received: (qmail 15590 invoked from network); 1 Mar 1999 10:39:32 -0000 Received: from pythagoras.physics.upatras.gr (150.140.159.71) by nic.upatras.gr with SMTP; 1 Mar 1999 10:39:32 -0000 Received: from demokritos.physics.upatras.gr by pythagoras.physics.upatras.gr with SMTP (1.36.108.4/16.2) id AA26838; Mon, 1 Mar 1999 13:37:39 +0200 Message-Id: <36DA6DFB.EE5FFE0A@physics.upatras.gr> Date: Mon, 01 Mar 1999 12:37:47 +0200 From: Christos Garoufalis X-Mailer: Mozilla 4.5 [en] (WinNT; I) X-Accept-Language: en Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: g94-CIS calculation Content-Type: text/plain; charset=iso-8859-7 Content-Transfer-Encoding: 7bit Dear CCLers Is there a way to perform a semiempirical (i.e. AM1) C.I. singlets calculation with gaussian94 ? thanks in advance Christos Garoufalis From chemistry-request@www.ccl.net Mon Mar 1 07:04:56 1999 Received: from hermes.aston.ac.uk (hermes.aston.ac.uk [134.151.79.46]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA10854 Mon, 1 Mar 1999 07:04:53 -0500 (EST) Received: from pharm78100.aston.ac.uk [134.151.78.100] by hermes.aston.ac.uk with smtp (Exim 1.82 #3) id 10HRRK-0003I9-00; Mon, 1 Mar 1999 12:04:50 +0000 Comments: Authenticated sender is From: "chaudash@aston.ac.uk" Organization: aston.ac.uk To: chemistry@www.ccl.net Date: Mon, 1 Mar 1999 12:07:37 +0000 MIME-Version: 1.0 Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Al in biological systems, Reply-to: chaudash@aston.ac.uk Priority: normal X-mailer: Pegasus Mail for Windows (v2.54) Message-Id: Hello ccl'ers, Thankyou for the numerous replies to my 1st question, namely any biological role of Al. I think what I really wanted to know was, is there any known biologically useful role of this metal in biological sytems, a bit like Fe being involved in oxygen transport among many other things. Another quick question, when undergoing optimisations in GAMESS, you get an energy value. Compunds optimised by semi-empirical (eg PM3) or ab initio (eg 3-21G) lead to totally different energy values, suggesting that the units are different. I believe that the energy term via ab intio is in Hartrees, so what are the units for semi empirical and how can I compare these to ab initio energy values Once again, Many thanks Shaqil From chemistry-request@www.ccl.net Mon Mar 1 07:12:13 1999 Received: from jmlopez.fam.cie.uva.es (aguado@jmlopez.fam.cie.uva.es [157.88.38.56]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA10911 Mon, 1 Mar 1999 07:12:02 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.9.1/8.9.1) id JAA07999 for chemistry@www.ccl.net; Sun, 28 Feb 1999 09:38:02 +0100 Date: Sun, 28 Feb 1999 09:38:02 +0100 From: Andres Aguado Message-Id: <199902280838.JAA07999@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: Data Recovery... Dear CCLers, I would like to obtain information as to what are the possibilities to retrieve the information of a hard disk that has broken down. The specific problem is the following: The hard disk is not recognized by the BIOS of any machine, so the problem seem not to be associated with the electronic part of the system. The disk simply does not exist at all!!. Several options concerning the opening of the disk are really expensive, at least at the best of my knowledge. Do you have any ideas as to what is the best (and if possible not too expensive) way to try retrieving the information in the disk?? The disk is a NEC with 2559.8 MB. Specifically it is DSE2550A. I know that this is a list for discussion about chemistry problems, so this kind of questions are perhaps out of place here. Nevertheless, your help (or any kind of useful information) would be greatly appreciated, and I would save a lot of physical and chemical information that is inside the disk!! Best regards, Andres Aguado. From chemistry-request@www.ccl.net Mon Mar 1 08:11:16 1999 Received: from jmlopez.fam.cie.uva.es (jmlopez.fam.cie.uva.es [157.88.38.56]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id IAA11281 Mon, 1 Mar 1999 08:11:10 -0500 (EST) Received: (from aguado@localhost) by jmlopez.fam.cie.uva.es (8.9.1/8.9.1) id KAA08102 for chemistry@www.ccl.net; Sun, 28 Feb 1999 10:37:07 +0100 Date: Sun, 28 Feb 1999 10:37:07 +0100 From: Andres Aguado Message-Id: <199902280937.KAA08102@jmlopez.fam.cie.uva.es> To: chemistry@www.ccl.net Subject: WORD to LaTeX... Dear All, Does anyone of you know of software that can convert a WORD file to a LaTeX file? Thanks in advance Andres Aguado. From chemistry-request@www.ccl.net Mon Mar 1 10:54:57 1999 Received: from nenuphar.saclay.cea.fr (nenuphar.saclay.cea.fr [132.166.192.7]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA13134 Mon, 1 Mar 1999 10:54:52 -0500 (EST) Received: from muguet.saclay.cea.fr (muguet.saclay.cea.fr [132.166.192.6]) by nenuphar.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with ESMTP id QAA03938 for ; Mon, 1 Mar 1999 16:56:03 +0100 (MET) Received: from styx.bruyeres.cea.fr (styx-e76.bruyeres.cea.fr [132.165.76.3]) by muguet.saclay.cea.fr (8.9.1a/8.9.1/CEAnet-relay-5.0.0.1) with SMTP id QAA13580; Mon, 1 Mar 1999 16:51:16 +0100 (MET) Received: by styx.bruyeres.cea.fr (CEANET-1.1+) id AA20868; Mon, 1 Mar 1999 16:54:47 +0100 Received: from indre.ripault.cea.fr(132.165.32.1) by styx via smap id sma020840; Mon Mar 1 16:54:05 1999 Received: from ripault.cea.fr (manse.ripault.cea.fr [132.165.32.9]) by ripault.cea.fr. (8.8.7/8.7.3) with ESMTP id QAA02672; Mon, 1 Mar 1999 16:53:39 +0100 Received: from manse.ripault.cea.fr (localhost [127.0.0.1]) by ripault.cea.fr (8.8.7/8.8.7) with SMTP id QAA29559; Mon, 1 Mar 1999 16:54:55 +0100 Sender: mathieu@ripault.cea.fr Message-Id: <36DAB84E.38A6904D@ripault.cea.fr> Date: Mon, 01 Mar 1999 15:54:54 +0000 From: Didier MATHIEU Organization: CEA - Le Ripault X-Mailer: Mozilla 3.01 (X11; I; Linux 2.0.32 i586) Mime-Version: 1.0 To: "E. Lewars" Cc: chemistry@www.ccl.net Subject: IR INTENSITIES per.syst.& Berry phase References: <199902280036.TAA25742@alchemy.chem.utoronto.ca> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit Content-Transfer-Encoding: 7bit reply to E. Lewars + additional question E. Lewars wrote: > ------------- > QUESTION: > Suppose we have, say H2O, and want to calc the relative intensities of > the asym and the sym stretching modes. In principle we can distort the geom > a little (as for H-F and H-Cl, above) and calc the change in dipole moment, > delta m. But what do we take as delta q when there is not just *one* simple > geometric parameter like r=(H--X)? I suppose either q is composite, or the > expression for I has several terms. As the distortion of a given mode q is given by the associated eigenvector U, then I think "delta q" should be taken as the magnitude (e.g. in Angstrom) of the distortion vector (delta q).U after conversion from the mass-weighted cartesian coordinates Q to the standard cartesian coordinates X. In other words, (delta q).U is given e.g. in amu^(1/2).Anqstroms. Each coordinate of this mass-weighted cartesian vector (delta q).U should be divided by the square root of the mass of the associated atom. This gives a new vector (delta x).X in angstroms, whose magnitude is (delta x). Then, delta m is the difference between the dipole calculated on the distorted geometry and the one calculated on the equilibrium geometry. To be consistent with to diatomic case, it seems to me, although I didn't studied to question in depth, that one should divide the magnitude of delta m (in Angstroms) by the magnitude of the vector (delta q).U in amu^(1/2).Angstroms, and then take the square of this quantity to obtain the intensity in Debye^2.Angstrom^-2.amu^-1. If this works, then such a scheme might be of practical value (instead of chain-rule differentiation of (delta m)/(elta q)) in the following context: * normal modes are available * IR intensities are to be obtained from a higher theoretical level as normal modes * one is only interested only in intensities in a restricted region of the spectrum Indeed, the IR intensities sought should be obtainable from a few dipole moment calculations for geometries distorted according to the few associated eigenvectors. BTW, I have another question related to IR intensities, more specially for periodic systems. It seems to me that some papers reported IR intensities for periodic systems in a purely classic approach, using a parameterized model for charge distribution (e.g. electro-optic parameters). On the other hand, I have been told that calculation of IR intensities of periodic systems should take into account the quantum "Berry Phase" (I don't know what it is) to make up for the lack of a proper definition of the "dipole moment" of such a system. How can one reconcile this requirement for the Berry phase with classical simulations for which no quantum concept is used ?? Thanks -- Didier MATHIEU CEA - Le Ripault, BP 16 37260 Monts (France) Tel. 33(0)2.47.34.41.85 From chemistry-request@www.ccl.net Mon Mar 1 11:20:59 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13477 Mon, 1 Mar 1999 11:20:53 -0500 (EST) Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA23676 for ; Mon, 1 Mar 1999 17:19:20 +0100 (CET) Date: Mon, 1 Mar 1999 17:19:20 +0100 From: Christian Pilger To: chemistry@www.ccl.net Subject: estimation of binding constants Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I did some docking on an enzyme/ligand complex. Now I have the problem of scoring the results i.e. prediction the binding constants for different enzyme-ligand alignments. I'd like to receive some information on this topic (molecular mechanics vs. quantum mechanics vs. empirical scoring schmemes...). Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 1 11:23:58 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA13537 Mon, 1 Mar 1999 11:23:32 -0500 (EST) Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id RAA23634 for ; Mon, 1 Mar 1999 17:22:06 +0100 (CET) Date: Mon, 1 Mar 1999 17:22:06 +0100 From: Christian Pilger To: chemistry@www.ccl.net Subject: conformational search on ring systems In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, is anybody aware of a software package that has a conformational search tool applicable to ring-systems ? Regards, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@www.ccl.net Mon Mar 1 12:48:52 1999 Received: from gw-uk1.ici.com (dns.ici-test.co.uk [134.239.84.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA15109 Mon, 1 Mar 1999 12:48:47 -0500 (EST) From: steve_rogers@ici.com Received: from GBEMX01.ICI-GROUP.COM (localhost.ici.com [127.0.0.1]) by gw-uk1.ici.com with SMTP id TAA23861 for ; Mon, 1 Mar 1999 19:43:00 GMT (envelope-from steve_rogers@ici.com) Received: from gbemx01.ici.com(134.239.75.10) by gw-uk1.ici.com via mwrap (4.0a) id xma023859; Mon, 1 Mar 99 19:43:00 GMT Received: by GBEMX01.ICI-GROUP.COM (Soft-Switch LMS 2.0) with snapi via NOTES1 id 0031900005921645; Mon, 1 Mar 1999 17:48:46 +0000 To: " - (052)CHEMISTRY(a)www.ccl.net" Subject: MOPAC Calculation on Radicals Message-ID: <0031900005921645000002L052*@MHS> Date: Mon, 1 Mar 1999 17:48:46 +0000 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 www.ccl.net id MAA15125 Hi, I'm interested in trying to model free radical alkene polymerisation reactions using MOPAC (AM1, PM3). There appear to be two possibilities for calculations on radicals - the Dewar half-electron method (which is invoked by the keyword DOUBLET) and UHF. The results differ by a few kcal/mol. Can anyone advise me which option is likely to give the best results for reaction thermodynamics and activation energies of a radical adding to a double bond? I'd also be interested in any comments on bond dissciation energies estimated by these methods. I'll summarise any replies. Thanks, Steve Rogers email: steve_rogers@ici.com From chemistry-request@www.ccl.net Mon Mar 1 14:29:31 1999 Received: from syr.edu (syr.edu [128.230.1.49]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA18910 Mon, 1 Mar 1999 14:29:31 -0500 (EST) Received: from gamera.syr.edu (dgallis@gamera.syr.edu [128.230.18.14]) by syr.edu (8.8.8/8.8.8) with SMTP id OAA26778 for ; Mon, 1 Mar 1999 14:25:02 -0500 (EST) Date: Mon, 1 Mar 1999 14:29:35 -0500 (EST) From: "Damian G. Allis" X-Sender: dgallis@gamera.syr.edu To: chemistry@www.ccl.net Subject: ESP/POLAR Problem in MOPAC97 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings! Thanks to all those who responded to my last question concerning asterisks in my MOPAC output (due to the numbers being larger than the output file was able and willing to print). I've another one for anybody. When I run a MOPAC input file with both POLAR and ESP, I get the POLAR output fine, but get "nan" for all of the ESP's for the atoms. When I run either seperately, I get the results I expect for each. Is there a known problem with running both ESP and POLAR in the same calculation, or is there some quick fix I'm not finding in the manual? thanks in advance, Damian Allis ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Home Address: | Chemistry Address: 349 Buckingham Ave. | 1-014,2-023,2-016e Center for Sci&Tech Syracuse, NY 13210 | Syracuse University email: dgallis@syr.edu | Syracuse, NY 13244 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#8^(= -)*-+-< everything about me: web.syr.edu/~dgallis/ Cornucopia Music: www.cornucopiamusic.com/ From chemistry-request@www.ccl.net Mon Mar 1 15:36:21 1999 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id PAA25436 Mon, 1 Mar 1999 15:36:19 -0500 (EST) Received: from redox.scripps.edu (redox.scripps.edu [137.131.240.50]) by relay1.scripps.edu (8.9.3/TSRI-3.0.1r) with ESMTP id MAA18699; Mon, 1 Mar 1999 12:36:18 -0800 (PST) Received: from localhost by redox.scripps.edu (8.9.1/TSRI-2.8) with SMTP id MAA04726; Mon, 1 Mar 1999 12:36:18 -0800 (PST) Date: Mon, 1 Mar 1999 12:36:17 -0800 (PST) From: "Jesus M. Castagnetto" Sender: jesusmc@scripps.edu To: Andres Aguado cc: chemistry@www.ccl.net Subject: Re: CCL:WORD to LaTeX... In-Reply-To: <199902280937.KAA08102@jmlopez.fam.cie.uva.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello Andres, Check the following URL: http://www.kfa-juelich.de/isr/1/texconv/pctotex.html You may also want to check www.ctan.org > Does anyone of you know of software that can convert a WORD file to a > LaTeX file? > > Thanks in advance > > Andres Aguado. -- Jesus M. Castagnetto - "Ken Zen Ichi-nyo" Program Project: http://www.scripps.edu/research/metallo/ Metalloprotein DB: http://metallo.scripps.edu/ Pilot Stuff: http://www.geocities.com/ResearchTriangle/Lab/1059/ From chemistry-request@www.ccl.net Mon Mar 1 18:54:12 1999 Received: from ftpbox.mot.com (ftpbox.mot.com [129.188.136.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id SAA04232 Mon, 1 Mar 1999 18:54:12 -0500 (EST) Received: [from mothost.mot.com (mothost.mot.com [129.188.137.101]) by ftpbox.mot.com (MOT-ftpbox 1.0) with ESMTP id RAA20359 for ; Mon, 1 Mar 1999 17:54:14 -0600 (CST)] Received: [from emailphx.sps.mot.com (emailphx.sps.mot.com [192.55.22.5]) by mothost.mot.com (MOT-mothost 1.0) with ESMTP id RAA08774 for ; Mon, 1 Mar 1999 17:54:13 -0600 (CST)] Received: from email.mot.com (zkorkin [223.189.20.185]) by act.sps.mot.com (8.8.6 (PHNE_14041)/8.8.6) with ESMTP id QAA00309 for ; Mon, 1 Mar 1999 16:54:12 -0700 (MST) Sender: korkin@act.sps.mot.com Message-ID: <36DB38B1.476B18CD@email.mot.com> Date: Mon, 01 Mar 1999 18:02:41 -0700 From: Anatoli Korkin X-Mailer: Mozilla 4.05C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: CCL Subject: Lennard-Jones Parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, Sorry, it is probably a text book question. Does anyone knows a good complilation of Lennard-Jones parameters, delta and epsilon, and paper(s)/review(s) of methods of their calculations. Thank you, Anatoli Korkin From chemistry-request@www.ccl.net Mon Mar 1 21:31:09 1999 Received: from atc.atccu.chula.ac.th (hung@atc.atccu.chula.ac.th [192.207.64.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA05274 Mon, 1 Mar 1999 21:31:04 -0500 (EST) Received: from localhost (hung@localhost) by atc.atccu.chula.ac.th (8.9.1/8.9.1) with ESMTP id JAA12905 for ; Tue, 2 Mar 1999 09:37:46 +0700 Date: Tue, 2 Mar 1999 02:37:46 +0000 ( ) From: Atchara Wijitkosoom To: CHEMISTRY@www.ccl.net Subject: Solvent Accessible Surface Area Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sir, I do a simulation of protein in order to compare the structure and its biological function. For my work, molecular dynamics have been performed to study dynamics structures of an enzyme at two different temperatures, 300 and 310.5K, using AMBER 5. One of my interesting properties is "Solvent accessible surface area" (SASA). The results show that SASA of the simulated structure at 310.5K is lower than that of the 300K. Is it strange result that the protein structure in aqueous solution at higher temperature has lower SASA than that of the lower temperature? Any comments will be appreciate. Sincerely yours, Hung