From yliu@mail.wesleyan.edu Fri Jul 10 17:05:43 1998 Received: from mail.wesleyan.edu (dns.wesleyan.edu [129.133.12.10]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA23072 Fri, 10 Jul 1998 17:05:43 -0400 (EDT) Received: from dkombo.wesleyan.edu (jellyfish.chem.wesleyan.edu [129.133.20.75]) by mail.wesleyan.edu (8.8.6/8.7.3) with SMTP id RAA28990; Fri, 10 Jul 1998 17:05:44 -0400 (EDT) Date: Fri, 10 Jul 1998 17:05:44 -0400 (EDT) Message-Id: <199807102105.RAA28990@mail.wesleyan.edu> X-Sender: yliu@wesleyan.edu X-Mailer: Windows Eudora Pro Version 2.1.2 Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: Yongxing Liu Subject: Experimental solvation free energy results for biomacromolecules Dear Friends, I would like to know if there is some information about experimental solvation free energy results for biomacromolecules(peptides, proteins, DNAs and RNAs). Please e-mail any resources from which I can get the related data. Thanks a lot in advance -------------------------------------------------------------------------- Yongxing Liu, Graduate Student | E-Mail: yliu@wesleyan.edu Department of Chemistry | Tel.:860-685-2777 Wesleyan University | Fax: 860-685-2211 Middletown CT 06459 | URL: http://ludwig.chem.wesleyan.edu/yliu --------------------------------------------------------------------------- From daizadeh@kappa.ucdavis.edu Fri Jul 10 23:01:51 1998 Received: from kappa.ucdavis.edu (kappa.ucdavis.edu [128.120.7.55]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id XAA29385; Fri, 10 Jul 1998 23:01:50 -0400 (EDT) Received: (from daizadeh@localhost) by kappa.ucdavis.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id UAA28589; Fri, 10 Jul 1998 20:01:46 -0700 From: "Iraj Daizadeh" Message-Id: <9807102001.ZM28587@kappa.ucdavis.edu> Date: Fri, 10 Jul 1998 20:01:46 -0700 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@www.ccl.net, Subject: Software on mpi or pvm. Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello. We have a couple of dec 500 au's (DEC unix 4.0c) and a sgi r10000 (6.2 irix) machine that we are considering parallelizing via mpi or pvm. I would like to know what chemistry software can utilize mpi or pvm. For example, it would be nice if there were dynamics packages such as Amber or Gromos that could use these tools; thus, one could run two classical trajectories simultaneously. If there is enough interest in this question, then I will post a summary of all results as is traditionally done on the CCL. Thank you in advance. Iraj. -- Iraj Daizadeh Department of Chemistry University of California One Shields Ave. Davis, CA 95616-5295 Phone: 530.754.8695 Fax: 530.752.8995 email: daizadeh@kappa.ucdavis.edu From info@molecules.com Mon Jul 13 11:59:40 1998 Received: from star.ccinet.com (root@ccinet.com [206.135.75.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id LAA11927 Mon, 13 Jul 1998 11:59:40 -0400 (EDT) Received: from molecules.com (ppp108.la1.ccinet.com [207.168.6.108]) by star.ccinet.com (8.8.5/8.7.3) with ESMTP id JAA02279; Mon, 13 Jul 1998 09:05:01 -0700 (PDT) Message-ID: <35AA2FD1.88C05185@molecules.com> Date: Mon, 13 Jul 1998 09:03:29 -0700 From: David Segrist X-Mailer: Mozilla 4.05 [en] (Win95; I) MIME-Version: 1.0 To: chemistry@www.ccl.net Subject: Re: CCL:CCL: looking for molecular modeling program on web or free References: <35A2DC15.EC2498DD@info.combichem.com> <35A54C0C.6C1D@uor.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Barbara Murray wrote: > I am part of a national committee running an undergraduate > pharmaceutical course on-line in the fall. We will be taking the > students through all the steps that are involved in getting a drug to > market. One of the things we want the students to do is to be able to > draw and look at their chosen molecule in some sort of modeling > program. Now, they don't really need to do calculations on this > molecule; just look at it and move it around. Calculations would only > be icing on the cake. May I suggest you look at these two options: 1 - Molecules-3D (v2.5) a very inexpensive 3D model building program ($49 student price) http://www.molecules.com/m3d_sefs.htm 2 - WebMolecules - an online VRML-based visualization Library (plug-in req'd) http://www.molecules.com/vrmlmols/index.html -- David Segrist Molecular Arts Technical Support ---------------------------------------------------------------- Molecular Arts Corporation | Hanover Corporate Centre, Suite 1000 | http://www.molecules.com 1532 East Katella Avenue | Main: (714) 634-8100 Anaheim, California 92805-6627 USA | FAX: (714) 634-1999 ---------------------------------------------------------------- From seabra@NPD.UFPE.BR Mon Jul 13 17:12:50 1998 Received: from NPD1.NPD.UFPE.BR (npd1.npd.ufpe.br [150.161.6.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA01939 Mon, 13 Jul 1998 17:12:32 -0400 (EDT) Received: from danon (Danon.DQF.UFPE.BR) by NPD.UFPE.BR (PMDF V5.1-4 #20469) with SMTP id <01IZD0JOHUF4000PGI@NPD.UFPE.BR> for chemistry@www.ccl.net; Mon, 13 Jul 1998 18:12:10 GMT-3 Date: Mon, 13 Jul 1998 18:22:53 -0300 From: Gustavo de Miranda Seabra Subject: Computer simulation methods To: Computational Chemistry List Reply-to: Gustavo de Miranda Seabra Message-id: <007701bdaea4$662719b0$7d05a196@danon.dqf.ufpe.br> MIME-version: 1.0 X-Mailer: Microsoft Outlook Express 4.72.2106.4 Content-type: multipart/alternative; boundary="----=_NextPart_000_0074_01BDAE8B.405B14C0" X-Priority: 3 X-MSMail-Priority: Normal X-MimeOLE: Produced By Microsoft MimeOLE V4.72.2106.4 Status: RO Content-Length: 2587 This is a multi-part message in MIME format. ------=_NextPart_000_0074_01BDAE8B.405B14C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, Does anyone have references that compare various simulation methods, like ab-initio, semi empirical, molecular dynamics and monte-carlo? Thanks very much. -------------------------------------------------------------------------= ------------------ Gustavo de Miranda Seabra MSc Student in Chemistry seabra@npd.ufpe.br Federal University of Pernambuco Brazil -------------------------------------------------------------------------= ------------------ ------=_NextPart_000_0074_01BDAE8B.405B14C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
    Does = anyone have=20 references that compare various simulation methods,
like=20 ab-initio, semi empirical, molecular dynamics and = monte-carlo?
 
    = Thanks very=20 much.
----------------------------------------------------------------= ---------------------------
       =             &= nbsp; =20 Gustavo de Miranda Seabra
MSc Student in=20 Chemistry          &nbs= p;      =20 seabra@npd.ufpe.br
Federal = University=20 of=20 Pernambuco          &nb= sp;           &nbs= p;     =20 Brazil
---------------------------------------------------------------= ----------------------------
------=_NextPart_000_0074_01BDAE8B.405B14C0-- From tajkhors@mbp-sgi7.inet.dkfz-heidelberg.de Tue Jul 14 09:38:59 1998 Received: from mbp-sgi7.inet.dkfz-heidelberg.de (mbp-sgi7.inet.dkfz-heidelberg.de [193.174.59.125]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id JAA13030 Tue, 14 Jul 1998 09:38:57 -0400 (EDT) Received: by mbp-sgi7.inet.dkfz-heidelberg.de (951211.SGI.8.6.12.PATCH1502/940406.SGI.AUTO) for chemistry@www.ccl.net id WAA02684; Tue, 14 Jul 1998 22:40:18 GMT From: "Emadeddin Tajkhorshid" Message-Id: <9807141540.ZM2682@mbp-sgi7.inet.dkfz-heidelberg.de> Date: Tue, 14 Jul 1998 15:40:09 -0700 Reply-To: E.Tajkhorshid@DKFZ-Heidelberg.de X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net (Computational Chemistry List) Subject: Dipole moment of a charged species Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Colleagues I have calculated two molecules using gas phase calculations and a number of different solvent models. They are both negatively charged species. Now the question is whether and how we can compare the dipole moments between these molecules and among different solvent models. I mean, the values, and also the directions, calculated for the dipole moment of a charged species are completely dependent on the origin of the coordinates. With this regard, how are the dipole moments calculated in quantom chemical calculations (particularly, I am interested in the reported values in the output of the Gaussian94 or DMOL programs)? And (how) can we use them for further analysis of the results or it is better to look at other properties like the atomic charges? Thanx in advance for your help. -- Emad ********************************************************************* E. Tajkhorshid German Cancer Research Center; DKFZ Tel: +49 6221 42 2340 Dept. Molecular Biophysics (H0200) FAX: +49 6221 42 2333 P.O.Box 101949 69009 Heidelberg, Germany Email: E.Tajkhorshid@DKFZ-Heidelberg.de ********************************************************************* * "Never express yourself more clearly than you think." -Niels Bohr * ********************************************************************* From dasf@elogica.com.br Tue Jul 14 14:07:55 1998 Received: from ceiun01.elogica.com.br (ceiun01.elogica.com.br [200.249.238.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA15489 Tue, 14 Jul 1998 14:07:51 -0400 (EDT) Received: from dasf.elogica.com.br (host218-60.elogica.com.br [200.249.218.60]) by ceiun01.elogica.com.br (8.8.7/8.8.7) with SMTP id PAA31899 for ; Tue, 14 Jul 1998 15:05:04 -0300 (GMT-0300) Message-Id: <3.0.32.19980714150711.0069cf98@elogica.com.br> X-Sender: dasf@elogica.com.br X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 14 Jul 1998 15:07:51 -0300 To: CHEMISTRY@www.ccl.net From: "=?iso-8859-1?Q?=22Dem=E9trio_A._da_Silva_Filho=22?=" Subject: GAMESS and TDHF 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 OAA15489 Dear CCL'ers, Does anybody know how GAMESS program calculate those quantities ISOTROPIC AVERAGE ALPHA, STATIC BETA-V and AVERAGE GAMMA VALUE in the TDHF routine? Could you give me some references? Thanks in advance, Demétrio Filho __________________________________________________ Tem um convite esperando por você em: http://www.elogica.com.br/users/dasf/convite.jpg __________________________________________________ From bausch@chem.vill.edu Tue Jul 14 17:25:46 1998 Received: from rs6chem.chem.vill.edu (rs6chem.chem.vill.edu [153.104.73.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id RAA17984 Tue, 14 Jul 1998 17:25:44 -0400 (EDT) Received: from [153.104.73.18] (bausch.chem.vill.edu [153.104.73.18]) by rs6chem.chem.vill.edu (8.8.5/8.8.5) with ESMTP id RAA07195 for ; Tue, 14 Jul 1998 17:25:42 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Tue, 14 Jul 1998 17:27:59 -0400 To: chemistry@www.ccl.net From: "Joseph W. Bausch" Subject: portland group compilers for linux/g94 Has anyone out there had success compiling G94 on an intel/linux box? If so, is the resulting code much faster or slower than that using the typical f2c/gcc route? I'll summarize if there is sufficient interest. Joe bausch@chem.vill.edu -------------------- From dkwmok@fg702-6.abct.polyu.edu.hk Tue Jul 14 21:51:54 1998 Received: from fg702-6.abct.polyu.edu.hk (fg702-6.abct.polyu.edu.hk [158.132.74.201]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id VAA19015 Tue, 14 Jul 1998 21:51:52 -0400 (EDT) Received: from cx802663.polyu.edu.hk ([158.132.31.49]) by fg702-6.abct.polyu.edu.hk (8.8.8/8.8.8) with SMTP id JAA03970 for ; Wed, 15 Jul 1998 09:52:18 +0900 (HKST) Message-Id: <3.0.2.32.19980715095923.0069819c@fg702-6.abct.polyu.edu.hk> X-Sender: dkwmok@fg702-6.abct.polyu.edu.hk X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.2 (32) Date: Wed, 15 Jul 1998 09:59:23 +0800 To: CHEMISTRY@www.ccl.net From: Daniel Mok Subject: G: Print option for normal coordinate. Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Dear all, I am doing some vibrational calculations which require the cartesian coord. of a normal mode. I try to get this with from the result of Gaussian. The output looks like: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A1 B2 A1 Frequencies -- 679.4127 1150.6407 1260.5904 Red. masses -- 17.7343 13.6835 13.8478 Frc consts -- 4.8231 10.6740 12.9652 IR Inten -- 3.7525 418.5434 120.7407 Raman Activ -- 0.0000 0.0000 0.0000 Depolar -- 0.0000 0.0000 0.0000 Atom AN X Y Z X Y Z X Y Z 1 6 0.00 0.00 -0.43 0.00 -0.87 0.00 0.00 0.00 -0.86 2 9 0.00 0.63 0.13 0.00 0.28 -0.21 0.00 -0.24 0.27 3 9 0.00 -0.63 0.13 0.00 0.28 0.21 0.00 0.24 0.27 Is there any option to make the number more precise? Daniel Dept. of Applied Biology and Chemical Technology Hong Kong Polytechnic University