From chemistry-request@server.ccl.net Thu Jul 12 03:26:17 2001 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6C7QA511205 for ; Thu, 12 Jul 2001 03:26:10 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=a3arzi) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 15KarO-00015f-00; Thu, 12 Jul 2001 09:26:06 +0200 Received: from localhost (a3arzi@localhost) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id JAA04548 for ; Thu, 12 Jul 2001 09:37:14 +0200 (GMT) Date: Thu, 12 Jul 2001 09:37:14 +0200 (GMT) From: Arturas Ziemys To: chemistry@ccl.net Subject: CCL: AutoDock parametrisation - some big questions In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, CCL'ers, AutoDock 3.0.5 parametrisation is unclear still: 1) I docked Fe anionic complex (-2) to some protein. Fe atom type parameters were included manually as it was suggested in AutoDock homepage. My docking energies were possitive. Could it be ? What is wrong ? Have anybody tested compound docking with Fe atom wit AD 3.x ? 2) Grid Paremter File (GPF) contains "sol_par" and "constant" keywors after each grid map 7 lines of interactions. I didn't came accross the purpose of these keywrds in manual. Could anybody explain the purpose of these keywords ? 3) Script utillities automatickly ganerates GPF with H-bond parameters assigned to O and S atom types with H. Why that do not happen with N ???? Looking forward for suggestions and any elucidations. Best wishes Arturas Z. From chemistry-request@server.ccl.net Thu Jul 12 04:02:20 2001 Received: from garuda.barc.ernet.in ([203.199.33.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6C82I512046 for ; Thu, 12 Jul 2001 04:02:18 -0400 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by garuda.barc.ernet.in (8.9.3/8.9.3) with ESMTP id NAA63739 for ; Thu, 12 Jul 2001 13:28:27 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id NAA18715 for ; Thu, 12 Jul 2001 13:40:09 +0530 Date: Thu, 12 Jul 2001 13:40:09 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: Subject: Bader'S AIM & Excited state Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi All, Has anybody used Bader's Atom-in-molecule analysis for excited state wavefunctions obtained from CI or MCSCF calculations. ************************************************************************ Dr. Tapan K. Ghanty Theoretical Chemistry Section Chemistry Division BARC, Trombay, Mumbai 400 085 India Phone: 91-22-5592675 ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Jul 12 10:32:17 2001 Received: from myamlak.ch.uj.edu.pl ([149.156.71.18]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6CEWH531083 for ; Thu, 12 Jul 2001 10:32:17 -0400 Received: from localhost (eilmes@localhost) by myamlak.ch.uj.edu.pl (8.9.3/8.9.3) with ESMTP id QAA24187 for ; Thu, 12 Jul 2001 16:30:23 +0200 (MET DST) Date: Thu, 12 Jul 2001 16:30:23 +0200 (MET DST) From: Andrzej Eilmes X-Sender: eilmes@myamlak.ch.uj.edu.pl To: chemistry@ccl.net Subject: self-consistent polarization in molecular dynamics Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL-ers, I'm trying to determine whether following thing can be done using available molecular dynamics programs (I haven't used any so far). We put an ion into solvent. When the ion is being solvated by the solvent molecules we take the induced dipoles into account: based on the molecular polarizabilities, we find dipole moments which electric field on the ion induces on solvent molecules. Induced dipoles lead to the correction to the electric field, so that we repeat the procedure until convergence is achieved (self- consistent polarization field). Then one can calculate the polarization energy for this ion/solvent system. I've found at the NWChem home page that there is a "polar" keyword which can turn on polariazation models. Is this related to my problem or does it mean something different? (BTW: what is the difference between "first" and "scf"? Does the first mean that we calculate induced dipoles only once, while the other means self-consistent procedure as described above). If you know about such kind of calculations could you give me references to the literature? Thanks in advance, Andrzej Eilmes -- ---------------------------------------------------------------- Dr Andrzej Eilmes eilmes@chemia.uj.edu.pl Faculty of Chemistry, Jagiellonian University, Krakow, Poland Phone: (48-12) 6336377 ext. 2030 Fax: (48-12) 6340515 ---------------------------------------------------------------- From chemistry-request@server.ccl.net Wed Jul 11 13:04:04 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6BH44529790 for ; Wed, 11 Jul 2001 13:04:04 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA04539; Wed, 11 Jul 2001 13:04:03 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B4C8217.F83A425B@cornell.edu> Date: Wed, 11 Jul 2001 12:43:04 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Help! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I'm having a problem in CHARMM. It's a three part problem and I'm trying to fix one part of it at a time. I think that I've fixed one part of it by myself, so I'm ready to move on to the second part, which is more difficult. The problem seems simple in theory, but it's driving me nuts. Here it is. I've built an alpha sugar in CHARMM and I have a patch in my RTF that is supposed to convert an alpha sugar into a beta sugar, which is what I want. Anyway, I can't get the patch to work. I guess I'm not sure where the patch statement is supposed to go. Here's how I have it in my input: READ SEQUENCE CARD 1 AGLC GENERATE GLUC ANGLES SETUP *PATCH BETA GLUC 1 SETUP PATCH MANN GLUC 1 SETUP The line with an asterisk is the one that isn't working and I'm not sure it's in the correct syntax. It says in the RTF as a comment that the BETA patch is to be used in the "generate" statement, but if do "GENERATE BETA blah blah SETUP, that doesn't work. Any help will be most appreciated. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Jul 12 00:05:22 2001 Received: from imo-d06.mx.aol.com ([205.188.157.38]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6C45M508897 for ; Thu, 12 Jul 2001 00:05:22 -0400 Received: from AKGhose@aol.com by imo-d06.mx.aol.com (mail_out_v30.22.) id g.31.177d4c25 (3980) for ; Thu, 12 Jul 2001 00:05:18 -0400 (EDT) From: AKGhose@aol.com Message-ID: <31.177d4c25.287e7bfd@aol.com> Date: Thu, 12 Jul 2001 00:05:17 EDT Subject: Book on Combinatorial Library Design To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="part1_31.177d4c25.287e7bfd_boundary" X-Mailer: AOL 6.0 for Windows US sub 10531 --part1_31.177d4c25.287e7bfd_boundary Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Folks: The book on combinatorial library design that we were editing for Marcel and Dekker has finally been published. Nearly fifty leading scientists from the industry and the academia have contributed twenty chapters on rational drug design and combinatorial library design, for this book. For a detail description, please check the following page: http://www.dekker.com/servlet/product/productid/0487-8 Thanks, Arup and Vis Amgen 805-447-3093 --part1_31.177d4c25.287e7bfd_boundary Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: 7bit Folks:

The book on combinatorial library design that we were editing for Marcel and
Dekker has finally been published. Nearly fifty leading scientists from the
industry and the academia have contributed twenty chapters on rational drug
design and combinatorial library design, for this book. For a detail
description, please check the following page:

http://www.dekker.com/servlet/product/productid/0487-8

Thanks,

Arup and Vis
Amgen
805-447-3093

--part1_31.177d4c25.287e7bfd_boundary-- From chemistry-request@server.ccl.net Wed Jul 11 15:19:06 2001 Received: from wodc7-1.uucp-gw.mail.uu.net ([199.171.54.178]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6BJJ6500945 for ; Wed, 11 Jul 2001 15:19:06 -0400 Received: from wodc7uc0.ffx.ops.us.uu.net by wodc7ug0.ffx.ops.us.uu.net with SMTP (peer crosschecked as: wodc7-1.uucp.uu.net [199.171.54.179]) id QQkxgf00711; Wed, 11 Jul 2001 19:18:59 GMT Message-Id: Received: from m10.UUCP by wodc7uc0.ffx.ops.us.uu.net with UUCP/RMAIL ; Wed, 11 Jul 2001 19:18:59 +0000 Received: by m10.gaussian.com; Wed, 11 Jul 2001 15:12:47 -0400 Received: by mousse.gaussian.com; Wed, 11 Jul 2001 14:48:42 -0400 From: gaussian.com!csd@gaussian.com (Cust. Service Doug) Subject: Re: CCL:EPR-3 basis set98 To: uunet!qtp.ufl.edu!fau%gaussian.com@uunet.uu.net (Stefan Fau) Date: Wed, 11 Jul 2001 14:48:42 -0400 (EDT) Cc: uunet!ccl.net!CHEMISTRY%gaussian.com@uunet.uu.net Reply-To: gaussian.com!help%gaussian.com@gaussian.com In-Reply-To: <08c901c108cb$effd6930$bbc0e380@qtp.ufl.edu> from "Stefan Fau" at Jul 9, 2001 07:07:33 pm X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dr. Fau, Here are the EPR-III basis sets in G98 input format. -N 0 S 5 1.00 0.2327485700D+05 0.2200000000D-03 0.3468183000D+04 0.1700000000D-02 0.7779884300D+03 0.9030000000D-02 0.2157197600D+03 0.3797000000D-01 0.6807803100D+02 0.1268200000D+00 S 1 1.00 0.2342439700D+02 0.1000000000D+01 S 1 1.00 0.8669376600D+01 0.1000000000D+01 S 1 1.00 0.3421753300D+01 0.1000000000D+01 S 1 1.00 0.9312565200D+00 0.1000000000D+01 S 1 1.00 0.3465688600D+00 0.1000000000D+01 S 1 1.00 0.1331153000D+00 0.1000000000D+01 S 1 1.00 0.4517000000D-01 0.1000000000D+01 P 4 1.00 0.8720500000D+02 0.8156000000D-02 0.2047800000D+02 0.6064200000D-01 0.6346300000D+01 0.2623890000D+00 0.2262400000D+01 0.7657020000D+00 P 1 1.00 0.8619000000D+00 0.1000000000D+01 P 1 1.00 0.3297800000D+00 0.1000000000D+01 P 1 1.00 0.1220500000D+00 0.1000000000D+01 P 1 1.00 0.4517000000D-01 0.1000000000D+01 D 1 1.00 0.1654000000D+01 0.1000000000D+01 D 1 1.00 0.4690000000D+00 0.1000000000D+01 F 1 1.00 0.1000000000D+01 0.1000000000D+01 **** -B 0 S 5 1.00 0.1062488800D+05 0.2430000000D-03 0.1587956300D+04 0.1911000000D-02 0.3579583100D+03 0.1010000000D-01 0.9926325900D+02 0.4217000000D-01 0.3147135600D+02 0.1362900000D+00 S 1 1.00 0.1092100300D+02 0.1000000000D+01 S 1 1.00 0.4070193500D+01 0.1000000000D+01 S 1 1.00 0.1617559900D+01 0.1000000000D+01 S 1 1.00 0.4272082500D+00 0.1000000000D+01 S 1 1.00 0.1663522000D+00 0.1000000000D+01 S 1 1.00 0.6656824000D-01 0.1000000000D+01 P 4 1.00 0.3999900000D+02 0.2090000000D-02 0.9340600000D+01 0.1621000000D-01 0.2835800000D+01 0.6539000000D-01 0.9911500000D+00 0.1942300000D+00 P 1 1.00 0.3760000000D+00 0.1000000000D+01 P 1 1.00 0.1458100000D+00 0.1000000000D+01 P 1 1.00 0.5609400000D-01 0.1000000000D+01 D 1 1.00 0.6610000000D+00 0.1000000000D+01 D 1 1.00 0.1990000000D+00 0.1000000000D+01 **** -O 0 S 5 1.00 0.3066450300D+05 0.2200000000D-03 0.4573201400D+04 0.1680000000D-02 0.1029552400D+04 0.8910000000D-02 0.2859047400D+03 0.3750000000D-01 0.9036965300D+02 0.1253800000D+00 S 1 1.00 0.3121957800D+02 0.1000000000D+01 S 1 1.00 0.1160776600D+02 0.1000000000D+01 S 1 1.00 0.4592759500D+01 0.1000000000D+01 S 1 1.00 0.1271171600D+01 0.1000000000D+01 S 1 1.00 0.4721401700D+00 0.1000000000D+01 S 1 1.00 0.1789653400D+00 0.1000000000D+01 S 1 1.00 0.5302000000D-01 0.1000000000D+01 P 4 1.00 0.1115400000D+03 0.2440000000D-02 0.2620600000D+02 0.1890000000D-01 0.8155600000D+01 0.8029000000D-01 0.2919600000D+01 0.2216200000D+00 P 1 1.00 0.1104700000D+01 0.1000000000D+01 P 1 1.00 0.4136800000D+00 0.1000000000D+01 P 1 1.00 0.1481000000D+00 0.1000000000D+01 P 1 1.00 0.5302000000D-01 0.1000000000D+01 D 1 1.00 0.2314000000D+01 0.1000000000D+01 D 1 1.00 0.6450000000D+00 0.1000000000D+01 F 1 1.00 0.1400000000D+01 0.1000000000D+01 **** > > Dear CCLers, > > I would like to do some calculations with the > EPR-3 basis set, but I did not find the actual > contraction coefficients (except for H and C). > I tried the Gaussian Basis Set Order Form > and mailed Prof. Barone, but he didn't answer > (maybe he's on vacation ...). > > I'd be grateful for any pointer to the EPR-3 basis > sets for B, N and O. Alternatively, I know that > G98, Rev. A9 has the basis set available, so I > wondered if somebody would be kind enough > to forward the basis set. The following input should > do the trick... > > Yours, > Stefan > > # scf/EPR-3 gfinput > > 0 1 > n > b 1,1.2 > o 2,1.1 1,179. > ______________________________________________________________________ > Dr. Stefan Fau | fau@qtp.ufl.edu > Quantum Theory Project | (352) 392-6714 > University of Florida > Gainesville, FL 32611-8435 > > > > -= 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 > > > > > -- Douglas J. Fox Technical Support Gaussian, Inc. help@gaussian.com From chemistry-request@server.ccl.net Thu Jul 12 05:52:31 2001 Received: from cuces.unisi.it ([193.205.4.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6C9qV509745 for ; Thu, 12 Jul 2001 05:52:31 -0400 Received: from CONVERSION-DAEMON.unisi.it by unisi.it (PMDF V6.0-24 #43309) id <01K5UCE4R89S000F3J@unisi.it> for chemistry@www.ccl.net; Thu, 12 Jul 2001 11:52:29 +0100 (MET) Received: from neriserv.chim.unisi.it (sysbiotech.bio-mol.unisi.it [192.167.124.8]) by unisi.it (PMDF V6.0-24 #43309) with ESMTPA id <01K5UCE1HEHM000EXW@unisi.it> for chemistry@www.ccl.net; Thu, 12 Jul 2001 11:52:29 +0100 (MET) Date: Thu, 12 Jul 2001 11:52:53 +0200 From: Andrea Bernini Subject: surface superposition To: Computational Chemistry list Message-id: <3B4D7375.E0D7402D@neriserv.chim.unisi.it> Organization: Dipartimento Biologia Molecolare - Siena MIME-version: 1.0 X-Mailer: Mozilla 4.51 [it] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en, it Dear CCLers, does anybody know of a computer program which does a superposition of two proteins based on the similarity of their surface shape, and possibly based also on surface properties such as hydrophilicity, hydrophobicity, charges? Thanks in advance, Andrea. ______________________________________________ Andrea Bernini, Dr Molecular Biology Dept. University of Siena Via Fiorentina 1, 53100 Siena, Italy Phone +39 577 234911 Fax +39 577 234903 From chemistry-request@server.ccl.net Thu Jul 12 10:09:57 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f6CE9v530737 for ; Thu, 12 Jul 2001 10:09:57 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id KAA25550; Thu, 12 Jul 2001 10:09:56 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3B4DAAC4.B765BD54@cornell.edu> Date: Thu, 12 Jul 2001 09:48:53 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: help! Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I'm having a problem in CHARMM. It's a three part problem and I'm trying to fix one part of it at a time. I think that I've fixed one part of it by myself, so I'm ready to move on to the second part, which is more difficult. The problem seems simple in theory, but it's driving me nuts. Here it is. I've built an alpha sugar in CHARMM and I have a patch in my RTF that is supposed to convert an alpha sugar into a beta sugar, which is what I want. Anyway, I can't get the patch to work. I guess I'm not sure where the patch statement is supposed to go. Here's how I have it in my input: READ SEQUENCE CARD 1 AGLC GENERATE GLUC ANGLES SETUP *PATCH BETA GLUC 1 SETUP PATCH MANN GLUC 1 SETUP The line with an asterisk is the one that isn't working and I'm not sure it's in the correct syntax. It says in the RTF as a comment that the BETA patch is to be used in the "generate" statement, but if do "GENERATE BETA blah blah SETUP", that doesn't work either. (CHARMM doesn't recognize what BETA is, it thinks it's a segment name, and not a patch name.) Any help will be most appreciated. Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Wed Jul 11 22:43:47 2001 Received: from web14309.mail.yahoo.com ([216.136.224.59]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f6C2hl508291 for ; Wed, 11 Jul 2001 22:43:47 -0400 Message-ID: <20010712024346.46711.qmail@web14309.mail.yahoo.com> Received: from [161.142.10.11] by web14309.mail.yahoo.com via HTTP; Wed, 11 Jul 2001 19:43:46 PDT Date: Wed, 11 Jul 2001 19:43:46 -0700 (PDT) From: rabia rabia Subject: FREE ENERGY-MIC VALUES-AUTODOCK3-INHIBITION CONSTANTS. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hi friends! i have calculated the estimated free energies of binding, inhibition constants of different ligands by docking them into the enzyme with the help of program AUTODOCK. for some ligands i have the experimental MIC values. i want to correlate my results with these experimental MIC values. any suggestion of how i can get the theoretical mic values from free energy or inhibition constants. another ? the program autodock3 gives inhibition constant values, any suggestion of how i can rank my ligands with respect to the inhibition constant...or how i can analyze it.... Thanx in advance for suggestions. rabia. UNIVERSITY. __________________________________________________ Do You Yahoo!? Get personalized email addresses from Yahoo! Mail http://personal.mail.yahoo.com/