From bear@ellington.Pharmacy.arizona.edu Thu Jun 18 12:37:02 1998 Received: from ellington.Pharmacy.arizona.edu (ellington.Pharmacy.Arizona.EDU [128.196.140.11]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id MAA08832 Thu, 18 Jun 1998 12:37:01 -0400 (EDT) Received: (from bear@localhost) by ellington.Pharmacy.arizona.edu (8.8.5/8.8.5) id JAA24383 for chemistry@www.ccl.net; Thu, 18 Jun 1998 09:37:01 -0700 (MST) Date: Thu, 18 Jun 1998 09:37:01 -0700 (MST) From: Soaring Bear Message-Id: <199806181637.JAA24383@ellington.Pharmacy.arizona.edu> To: chemistry@www.ccl.net Subject: cobalt parameters Howdy: Has anyone modeled cobalt containing enzymes? I would very much appreciate seeing what basis sets (and refs) folks have used for ab initio of cobalt local environment and what parameters have been used for minimization/dynamics. thanks, SOARING BEAR PhD bear@pharmacy.arizona.edu Computational Medicinal Chemistry; Molecular Modeling; Pharmacognosy Protein & DNA Structural Biology; Cancer Biochemistry; Informatics; QSAR http://ellington.pharmacy.arizona.edu/~bear/resume.html currently seeking employment From chemtw@showme.missouri.edu Fri Jun 19 13:18:12 1998 Received: from mail.missouri.edu (mail.missouri.edu [128.206.2.169]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id NAA16723 Fri, 19 Jun 1998 13:18:12 -0400 (EDT) Received: from sp2n09.missouri.edu (sp2n09.missouri.edu [128.206.2.17]) by mail.missouri.edu (8.9.0/8.9.0) with ESMTP id MAA118564 for ; Fri, 19 Jun 1998 12:18:13 -0500 Received: from localhost (chemtw@localhost) by sp2n09.missouri.edu (8.9.0/8.9.0) with SMTP id MAA09816 for ; Fri, 19 Jun 1998 12:17:21 -0500 X-Authentication-Warning: sp2n09.missouri.edu: chemtw owned process doing -bs Date: Fri, 19 Jun 1998 12:17:21 -0500 (CDT) From: Troy Wymore X-Sender: chemtw@sp2n09.missouri.edu To: chemistry@www.ccl.net Subject: CHARMM/SHAKE problem Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII CHARMM people, I am having a problem minimizing or running dynamics using CHARMM version 25b2 on NCSA's Power Challenge Array. When running the same job using CHARMM version 24b2 on our university's Power Challenge, everything works fine. At NCSA I was having problems with the SHAKE constraints on the bonds to hydrogen. Looking at the starting coordinates, showed that all bonds to hydrogen were of reasonable bond lengths, due to an earlier minimization on our own computer. Currently I am trying to minimize this system at NCSA and SHAKE has not failed this time, but the energy of the system is extremely high, though the starting coordinates come from a converged ABNR minimization done on our own computer. Are there some new parameters that need to be specified using the new version of CHARMM with regards to SHAKE? My SHAKE command is : shake bonh tol 1.0e-07 para I am also using crystal to define the PBCs. The system is a solvated lipid aggregate. Any help would be much appreciated. **************************************** Troy Wymore Department of Chemistry University of Missouri-Columbia Columbia, MO 65211 e-mail: chemtw@showme.missouri.edu http://www.missouri.edu/~chemtw/troy.html ***************************************** From armel@fluo.univ-lemans.fr Sat Jun 20 06:10:55 1998 Received: from aviion.univ-lemans.fr (aviion.univ-lemans.fr [192.93.244.3]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA19622 Sat, 20 Jun 1998 06:10:50 -0400 (EDT) Received: from fluo.univ-lemans.fr by aviion.univ-lemans.fr (SMI-8.6/SMI-SVR4) id MAA27081; Sat, 20 Jun 1998 12:07:36 +0100 Received: from pcb4122.univ-lemans.fr by fluo.univ-lemans.fr (AIX 3.2/UCB 5.64/4.03) id AA20507; Sat, 20 Jun 1998 13:11:23 +0200 Message-Id: <3.0.32.19980620121344.006d4884@fluo.univ-lemans.fr> X-Sender: armel@fluo.univ-lemans.fr X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Sat, 20 Jun 1998 12:13:52 +0200 To: chemistry@www.ccl.net From: Armel Le Bail Subject: Would you please predict those crystal structures ?-) 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 GAA19622 Hi, A challenge for you. 10 days are remaining for the ab initio crystal structure determination of the 2 samples below before the SDPD Round Robin deadline : http://fluo.univ-lemans.fr:8001/SDPDRR/ Sample 1 [Co(NH3)5CO3]NO3.H2O (guessing the shape of structure fragments is possible) Crystal system: monoclinic Cell : a = 7.673A, b = 9.628 A, c = 7.077 A, beta = 106.28° Space groups : P21/m or P21 Sample 2 C22H24N2O8.HCl (the molecular formula can be found easily) Crystal system: orthorhombic Cell : a = 10.981 A, b = 12.853 A, c = 15.733 A, Space group : P212121 Best wishes, Armel Le Bail - Universite du Maine, Laboratoire des Fluorures, CNRS ESA 6010, Av. O. Messiaen, 72085 Le Mans cedex 9, France http://fluo.univ-lemans.fr:8001/ http://www.cybercable.tm.fr/~cristal/welcome.html From jola@neon.ch.pwr.wroc.pl Sat Jun 20 12:18:35 1998 Received: from neon.ch.pwr.wroc.pl (neon.ch.pwr.wroc.pl [156.17.2.212]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id MAA20713 Sat, 20 Jun 1998 12:18:32 -0400 (EDT) Received: from neon.ch.pwr.wroc.pl (localhost [127.0.0.1]) by neon.ch.pwr.wroc.pl (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id SAA03947 for ; Sat, 20 Jun 1998 18:14:35 +0200 Sender: jola@neon.ch.pwr.wroc.pl Message-ID: <358BDFEB.41C6@neon.ch.pwr.wroc.pl> Date: Sat, 20 Jun 1998 18:14:35 +0200 From: Jolanta Grembecka Organization: Wroclaw University of Technology X-Mailer: Mozilla 3.01SGoldC-SGI (X11; I; IRIX 6.3 IP32) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: zinc charges Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone: I am going to carry out some simulation of leucine aminopeptidase (which is zinc containing enzyme) with its inhibitor (phosphonic analogue of leucine) in CFF97 force field. I would like to calculate ab initio the charges for two zinc ions (which are very close each other in the active center of the enzyme - the distance 3A) and for zinc ligands (mainly glutamic and aspatric acids which have been replaced in my system by formic acids and inhibitor). I tried to calculate the charges for such system using 3-21G and 6-311G* basis sets and I obtained very different results from the calculations. Using 3-21G basis set the zinc charges values were about +0.8 u.a. and using 6-311G* basis set these values were about +1.7 u.a. Which of them are correct? Could anyone tell me what method and basis set should I use to obtain the most appropriate charges for this system remembering that the system contains 49 atoms (616 basis functions for 6-311G* basis set). Jolanta Grembecka