From BOTTA@unisi.it Wed Dec 21 05:26:26 1994 Received: from ICNUCEVX.CNUCE.CNR.IT for BOTTA@unisi.it by www.ccl.net (8.6.9/930601.1506) id FAA10697; Wed, 21 Dec 1994 05:07:01 -0500 From: Received: from SIVAX (BOTTA@SIVAX@DECNET-MAIL ) by icnucevx.cnuce.cnr.it (PMDF V4.3-13 #6635) id <01HKWIGKVS5SNSJ9XF@icnucevx.cnuce.cnr.it>; Wed, 21 Dec 1994 10:59:06 +0100 (MET) Date: Wed, 21 Dec 1994 09:37 +0100 (MET) Subject: PROBLEMS WITH MNDO-ESP CHARGE CALCULATION To: CHEMISTRY@ccl.net Message-id: <01HKWIKRIPVCNSJ9XF@icnucevx.cnuce.cnr.it> Content-transfer-encoding: 7BIT X-Original-To: CHEMISTRY@ccl.net Dear Netters, this is my first time writing at the computer chemistry list, so I hope I won't make mistakes! I'm involved in a strange problem: I need a set of extremely refined charges for this simple fragment: 1,5 dimetoxy-2,4 dimethyl-benzene; unfortunately I don't have the ab-initio program GAUSSIAN, so I used MOPAC-MNDO choosing the ESP option. The problem is that the partial charges obtained for the two oxigens of the metoxy groups are less negative than the one on the C5 atom (-0. 33 -0.45 respectively). Should it be theorically correct? Consider that I never obtain this result when using MOPAC_AM1 without the ESP option. Please, send messages to me and I will post for the list. Thank you in advance for any suggestion. Vega Masignani E-mail: botta@sivax.unisi.it From bonvoisi@cemes.cemes.fr Wed Dec 21 08:27:36 1994 Received: from cix.cict.fr for bonvoisi@cemes.cemes.fr by www.ccl.net (8.6.9/930601.1506) id IAA11868; Wed, 21 Dec 1994 08:22:33 -0500 Received: from cemes.cemes.fr by cix.cict.fr; Wed, 21 Dec 94 14:26:34 +0100 Received: by cemes.cemes.fr; Wed, 21 Dec 94 14:20:34 EST From: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques) Message-Id: <9412211320.AA14815@cemes.cemes.fr> Subject: Molecular Orbital To: chemistry@ccl.net (CCL Computational Chemistry) Date: Wed, 21 Dec 94 14:20:32 EST Cc: bonvoisi@cemes.cict.fr (Jacques Bonvoisin) X-Mailer: ELM [version 2.3 PL11] Dear Netters, Recently I asked for programs able to draw or view Molecular Orbital issued from MOPAC type calculations. I got several answers and thanks for that. I wanted free and ftp'able programs. Among them, there were : PSI88, MOLDEN, MOPLOT2, SciAn, EDMOL. For my purpose, the best I try so far was PSI88 although there is some problem: - It works fine for small molecules ie with atoms numbers in the order of 10-20, but it did not seem to work with bigger molecules ie 40-50 atoms. Does somebody know why ? - Is there any mailing-list associated with this program ? I am trying to test the other cited-above program to see if they do better. Greetings. Bye. -- +----------------------------------------------------------------+ | Jacques BONVOISIN | | CNRS/CEMES-LOE Tel : +33 62 25 78 52 | | 29 , rue Jeanne Marvig Fax : +33 62 25 79 99 | | F-31055 Toulouse Cedex Email: bonvoisi@cemes.fr | +----------------------------------------------------------------+ From sage.Syntex.Com!dan@synseer.Syntex.Com Wed Dec 21 11:26:30 1994 Received: from olivea.ATC.Olivetti.Com for sage.Syntex.Com!dan@synseer.Syntex.Com by www.ccl.net (8.6.9/930601.1506) id LAA14581; Wed, 21 Dec 1994 11:17:59 -0500 Received: by olivea.ATC.Olivetti.Com (5.65/1.34) id AA12561; Wed, 21 Dec 94 08:16:12 -0800 Received: from synseer.Syntex.Com by olivea.ATC.Olivetti.Com (4.1/SMI-4.1) id AA12558; Wed, 21 Dec 94 08:16:10 PST Received: from dnsa5-1.Syntex.Com.Syntex.Com by Syntex.Com (4.1/SMI-4.1) id AA03369; Wed, 21 Dec 94 08:13:06 PST Received: from sage.syntex.com by dnsa5-1.Syntex.Com.Syntex.Com (4.1/SMI-4.1) id AA19555; Wed, 21 Dec 94 08:15:24 PST Received: by sage.syntex.com (931110.SGI/921111.SGI.AUTO) for @synseer.syntex.com:chemistry@ccl.net id AA15283; Wed, 21 Dec 94 08:12:14 -0800 From: "Dr. Daniel L. Severance" Message-Id: <9412210812.ZM15281@sage.syntex.com> Date: Wed, 21 Dec 1994 08:12:12 -0800 In-Reply-To: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques) "CCL:Molecular Orbital" (Dec 21, 2:20pm) References: <9412211320.AA14815@cemes.cemes.fr> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: bonvoisi@cemes.cemes.fr (Bonvoisin Jacques), chemistry@ccl.net Subject: Re: CCL:Molecular Orbital Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 Hi, In the psi1.f portion of PSI88, there are two parameter statements: PARAMETER (MAXATM=50) PARAMETER (MAXORB=200) The first for the maximum number of atoms which can be used, but the second parameter also determins how many atoms you can use. It is the maximum number of orbitals allowed, and will need to be increased, especially if you are doing gaussian type basis sets. Edit psi1.f and make a global change of MAXORB=200 to MAXORB=500. If you aren't short on memory you can make it 1000 instead of 500. One array will increase in size from 160K to 1MB at 500, and 4MB using a value of 1000. Then recompile and that should fix the problem. I see that I didn't do as much range checking as I should have when I wrote the program :-b Apologies for that. Good luck! -- Dr. Daniel L. Severance dan@sage.syntex.com Staff Researcher Work phone: (415) 354-7509 Syntex Discovery Research Home phone: (415) 969-5818 R6W-002 Fax (Work): (415) 354-7363 3401 Hillview Ave Palo Alto, CA 94303 From mrigank@imtech.ernet.in Wed Dec 21 19:03:52 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id SAA01150; Wed, 21 Dec 1994 18:34:49 GMT Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id AAA05044 for chemistry@ccl.net; Thu, 22 Dec 1994 00:04:48 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA04730; Wed, 21 Dec 94 23:55:43+050 Message-Id: <9412211855.AA04730@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 20 Dec 94 23:43:32 +0530 Date: Tue, 20 Dec 94 23:43:32 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:Monte Carlo Code X-Vms-Mail-To: CHEM ==> ==> Does anyone know where one can get a Monte Carlo version of standard ==>molecular mechanics methods such as Amber, or one of the MM series? ==> ==>Thanks in advance ==> ==>Dr. Ross Underhill ==>Royal Military College of Canada ==>Kingston, Ontario ==>(613) 541-6000 X6175 BOSS by Willam Jorgensen is probably what you are looking for. He can be reached at bill@doctor.chem.yale.edu. I costs $500 for academic people. Hope this helps Mrigank ---- /Mrigank \/ Phone +91 172 40957 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 40958, +91 172 28032 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran From mrigank@imtech.ernet.in Wed Dec 21 19:11:48 1994 Received: from sangam.ncst.ernet.in for mrigank@imtech.ernet.in by www.ccl.net (8.6.9/930601.1506) id SAA01151; Wed, 21 Dec 1994 18:34:55 GMT Received: (from root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id AAA05048 for chemistry@ccl.net; Thu, 22 Dec 1994 00:04:49 +0500 Received: from imtech.UUCP by doe.ernet.in (4.1/SMI-4.1-MHS-7.0) id AA04742; Wed, 21 Dec 94 23:55:46+050 Message-Id: <9412211855.AA04742@doe.ernet.in> Received: by imtech.ernet.in (DECUS UUCP w/Smail); Tue, 20 Dec 94 23:44:48 +0530 Date: Tue, 20 Dec 94 23:44:48 +0530 From: Mrigank To: chemistry@ccl.net Subject: RE: CCL:molecular display program X-Vms-Mail-To: CHEM ==>Hi, ==> ==>Is there a public-domain molecular display program which can ==>be made to repetitively read and re-read a pdb file? ==>The idea is to have an MD program dump conformations ==>into the file every n steps, and have the display ==>pick these up and display them for a near-real-time ==>display of the trajectory. ==> ==>Thanks, ==> ==>Mike Gilson MolPic can solve your problem if you are using DEC Workstaions [ultrix or OSF/1] or have PHIGS support. NEAR REAL TIME is not possible. BTW, what do you mean by that. One ps will take much much .... more time than a ps. Mrigank ---- /Mrigank \/ Phone +91 172 40957 \ \Institute of Microbial Technology /\ Email: mrigank@imtech.ernet.in / /Sector 39A, \/ FAX: +91 172 40958, +91 172 28032 \ \Chandigarh 160 014 India. /\ / \//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\//\// -- When I feed the poor, they call me saint. When I ask why the poors do not have food, they call me communist - Archbishop Camaran -------This is added Automatically by the Software-------- -- Original Sender Envelope Address: gilson@indigo12.carb.nist.gov -- Original Sender From: Address: gilson@indigo12.carb.nist.gov CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73 Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV