From romano@bellatrix.pcl.ox.ac.uk Fri Jan 23 07:16:55 1998 Received: from oxmail4.ox.ac.uk for romano@bellatrix.pcl.ox.ac.uk by www.ccl.net (8.8.3/950822.1) id GAA28345; Fri, 23 Jan 1998 06:30:41 -0500 (EST) Received: from joule.pcl (actually host joule.pcl.ox.ac.uk) by oxmail4 with SMTP (PP) with ESMTP; Fri, 23 Jan 1998 11:29:30 +0000 Received: from bellatrix.pcl (bellatrix.pcl [163.1.35.131]) by joule.pcl (8.8.6/8.6.5) with SMTP id LAA15318 for <@joule.pcl:CHEMISTRY@www.ccl.net>; Fri, 23 Jan 1998 11:30:28 GMT Received: by bellatrix.pcl (940816.SGI.8.6.9/940406.SGI.AUTO) for CHEMISTRY@www.ccl.net id LAA18045; Fri, 23 Jan 1998 11:18:09 GMT From: romano@bellatrix.pcl.ox.ac.uk (Romano Kroemer) Message-Id: <199801231118.LAA18045@bellatrix.pcl> Subject: Need data on amino acids in the gas phase To: CHEMISTRY@www.ccl.net Date: Fri, 23 Jan 1998 11:18:08 +0000 (GMT) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Dear all, does anyone have (or know where to find) data on the conformations of amino acids in the gas phase, either from calculations or experiments? I am particularily interested in aromatic aa's, but any input is welcome. I look forward to many responses and would like to take this opportunity to thank you in advance for your help. RTK -- =============================================================================== Dr. Romano T. Kroemer Phys. & Theoret. Chem. Lab. University of Oxford South Parks Rd. | Tel: ++44-1865-275475 Oxford OX1 3QZ | Fax: ++44-1865-275410 England, U.K. | Email: romano@bellatrix.pcl.ox.ac.uk =============================================================================== From ccl@www.ccl.net Fri Jan 23 13:17:11 1998 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id MAA00770; Fri, 23 Jan 1998 12:41:57 -0500 (EST) Received: from SIUCVMB.SIU.EDU for TAPASKAR@SIUCVMB.SIU.EDU by bedrock.ccl.net (8.8.6/950822.1) id MAA23026; Fri, 23 Jan 1998 12:41:56 -0500 (EST) Message-Id: <199801231741.MAA23026@bedrock.ccl.net> Received: from SIUCVMB.SIU.EDU by SIUCVMB.SIU.EDU (IBM VM SMTP V2R2) with BSMTP id 7234; Fri, 23 Jan 98 11:41:29 CST Date: Fri, 23 Jan 98 11:39:44 CST From: "Tapas Kar, Ph.D, Asst. Scientist" To: chemistry@ccl.net Subject: Problem with rasscf calculation in MOLCAS Status: RO Content-Length: 6375 Hi, I am interested to calculate the S1/T1 states of Malonaldehyde. But I got some problem to get a pure S1 state. I had to take an average of two states. The input and part of the RASSCF output are enclosed. In this particular input I took the 50-50 average. An average of 10-90 or 90-10 does not lead to a pure S1 state. By pure S1 state I mean, the weight of the configuration 17 of rooti 2 should be greater than 0.9. And alaways I am getting a value in the range of 0.72 - 0.77. configuration 17 coefficient .872244 weight .760810 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 Natural orbitals and occupation numbers for root 2 Occupation numbers for symmetry 1 1.971424 .028050 Occupation numbers for symmetry 2 1.932725 1.375825 .629482 .054140 .008354 values in 2nd and 3rd col. of symmetry 2 should be arround 1.0 instead of 1.37 and 0.63. Please suggest me how I can improve the result. Thanks for your attention and cooperation, Tapas Kar Rasscf Input file &RASSCF &END Title Malonaldehyde pt2 Iterations 50 50 LEVSHFT 0.0 Nactel 6 0 0 Inactive 15 1 Ras2 2 5 symmetry 1 Spin 1 CIRoot 2 2 1 2 1 1 LumOrb End of input Rasscf Output******* Convergence after 27 iterations 28 2 4 0 -265.21293103 -.18E-09 16 34 1 -.11E-05 .31E-04 .00 1.22 QN YES .05 .00 wave function printout: Split Graph format in parenthesis: midvertex, upper-walk symmetry, upper and lower-walk serial numbers ************************************************************************************************************************ printout of CI-coefficients larger than .05 for root 1 energy= -265.309683 configuration 16 coefficient .898219 weight .806796 ( 3:1: 1: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 2 0 0 0 spin-coupling 3 0 3 3 0 0 0 configuration 17 coefficient -.321184 weight .103159 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 configuration 18 coefficient -.087996 weight .007743 ( 3:1: 3: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 2 0 0 spin-coupling 3 0 3 0 3 0 0 configuration 19 coefficient .123153 weight .015167 ( 3:1: 4: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 0 1 0 spin-coupling 3 0 3 1 0 2 0 printout of CI-coefficients larger than .05 for root 2 energy= -265.116179 configuration 16 coefficient .350120 weight .122584 ( 3:1: 1: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 2 0 0 0 spin-coupling 3 0 3 3 0 0 0 configuration 17 coefficient .872244 weight .760810 ( 3:1: 2: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 1 1 0 0 spin-coupling 3 0 3 1 2 0 0 configuration 18 coefficient -.059916 weight .003590 ( 3:1: 3: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 2 0 0 spin-coupling 3 0 3 0 3 0 0 configuration 20 coefficient -.168264 weight .028313 ( 3:1: 5: 2) symmetry 1 1 2 2 2 2 2 occupation 2 0 2 0 1 1 0 spin-coupling 3 0 3 0 1 2 0 Natural orbitals and occupation numbers for root 1 Occupation numbers for symmetry 1 1.978993 .020544 Occupation numbers for symmetry 2 1.944668 1.904601 .094931 .052511 .003753 Natural orbitals and occupation numbers for root 2 Occupation numbers for symmetry 1 1.971424 .028050 Occupation numbers for symmetry 2 1.932725 1.375825 .629482 .054140 .008354 Wave function specifications: ----------------------------- Number of closed shell electrons 32 Number of electrons in active shells 6 Max number of holes in RAS1 space 0 Max number of electrons in RAS3 space 0 Number of inactive orbitals 16 Number of active orbitals 7 Number of secondary orbitals 30 Spin quantum number .0 State symmetry 1 Orbital specifications: ----------------------- Symmetry species 1 2 Frozen orbitals 0 0 Inactive orbitals 15 1 Active orbitals 2 5 RAS1 orbitals 0 0 RAS2 orbitals 2 5 RAS3 orbitals 0 0 Secondary orbitals 26 4 Deleted orbitals 0 0 Number of basis functions 43 10 CI expansion specifications: ---------------------------- Number of configuration state fnc. 260 Number of determinants 625 Number of root(s) required 2 CI roots used 1 2 weights .5000 .5000 highest root include in the CI 2 Final optimization conditions: ------------------------------ Average CI energy -265.21293103 RASSCF energy -265.21293103 Super-CI energy .00000000 RASSCF energy change .00000000 Max change in MO coefficients -.503E-04 Max non-diagonal density matrix elemen .312E-04 Maximum BLB matrix element -.111E-05 (orbital pair 16, 34 in symmetry 1) Final state energy(ies): ------------------------ root number 1 E = -265.30968309 a.u. root number 2 E = -265.11617898 a.u. From ccl@www.ccl.net Fri Jan 23 14:16:57 1998 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id NAA01244; Fri, 23 Jan 1998 13:25:38 -0500 (EST) Received: from phoenix.engin.umich.edu for nakiya@engin.umich.edu by bedrock.ccl.net (8.8.6/950822.1) id NAA24653; Fri, 23 Jan 1998 13:25:36 -0500 (EST) Received: from localhost (nakiya@localhost [127.0.0.1]) by phoenix.engin.umich.edu (8.8.7/8.8.7) with SMTP id NAA12190 for ; Fri, 23 Jan 1998 13:25:37 -0500 (EST) Date: Fri, 23 Jan 1998 13:25:36 -0500 (EST) From: Naoko Akiya To: chemistry@ccl.net Subject: CCL: parameters for H2O2 In-Reply-To: <199801221642.LAA07760@bedrock.ccl.net> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Does anyone know where I can get the OPLS parameters for hydrogen peroxide or similar compounds? Thank you for your help. =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Naoko Akiya nakiya@engin.umich.edu University of Michigan Dept. of Chemical Engineering phone (313) 764-7121 Ann Arbor, MI 48109-2136 fax (313) 763-0459 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From dalke@zed.mag.com Sun Jan 25 20:35 EST 1998 Received: from zed.mag.com for dalke@zed.mag.com by www.ccl.net (8.8.3/950822.1) id UAA12088; Sun, 25 Jan 1998 20:35:01 -0500 (EST) Received: (from mail@localhost) by zed.mag.com (8.8.5/8.7.2) id RAA11101 for ; Sun, 25 Jan 1998 17:35:00 -0800 Received: from UNKNOWN(198.211.208.86), claiming to be "tull" via SMTP by zed, id smtpda11099; Mon Jan 26 01:34:57 1998 Date: Sun, 25 Jan 1998 17:35:00 -0800 Message-Id: <199801260135.RAA11101@zed.mag.com> From: Andrew Dalke To: chemistry-request@www.ccl.net Subject: surface area and volume calculations Reply-to: dalke@mag.com Hello, I've been looking for programs or libraries that calculate molecular surface area and volume. I've found quite a few (eg, NACCESS) but none meet the "free"-ness criterion I have. Let me explain that. I am one of the developers of VMD, a free molecular visualization, animation and analysis program for unix machines (see http://www.ks.uiuc.edu/Research/vmd/). VMD is one of the few visualization programs I've seen that is free, does not require a license, come with complete source code, is redistributable and allows non-academic use. I would like to add suface area and volume information to the VMD but don't want to go and reimplement (and test) methods like Lee and Richards. I would rather incorporate code from an existing program or library. That calls for code that itself meets the liberal copyright of VMD, and I haven't found any. It is not necessary that VMD distribution include the source code to this program if we can include the program in binary form. We do this for Frishman's secondary structure determination program STRIDE and Varshney's molecular surface program SURF and have had no compliants. Does anyone on this list know of such beast? Andrew --- Not speaking for the Molecular Applications Group.