From chemistry-request@server.ccl.net Tue Oct 31 02:17:50 2000 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA20369 for ; Tue, 31 Oct 2000 02:17:46 -0500 Received: from iris.sipp.ac.cn (202.127.25.133) by iris.sipp.ac.cn (EMWAC SMTPRS 0.81) with SMTP id ; Tue, 31 Oct 2000 15:21:34 +0800 Sender: user@ccl.net Message-ID: <39FE71C8.7A2BA7E1@iris.sipp.ac.cn> Date: Tue, 31 Oct 2000 15:16:25 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.51C-SGI [en] (X11; I; IRIX 6.3 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: where to get CPMD Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, everyone: I read an article about modeling enzyme mechanism using CPMD, I am interested in that program, can anyone tell me where I can get it. Thanks. Regards, mao ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | Xiang Mao | | Lab of Molecular Regulation for Microbial Secondary Metabolism | | Shanghai institute of Plant Physiology, Academia Sinica | | 300 Fenglin Road, Shanghai, China, 200032 | | Tel: +86-21-64042090-4791 | | Fax: +86-21-64042385 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From chemistry-request@server.ccl.net Tue Oct 31 05:37:24 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA21372 for ; Tue, 31 Oct 2000 05:37:23 -0500 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id MAA39874 for ; Tue, 31 Oct 2000 12:06:01 +0100 (CET) Date: Tue, 31 Oct 2000 12:06:00 +0100 From: Christian Pilger To: chemistry@server.ccl.net Subject: vibrational analysis with g98 In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, in order to extent the parameters in the AMBER force field to some small organic molecules, I want to get individual force constants for bond- and angle-vibrations from g98 calculations. Can somebody tell me how to get this information out of the g98-output files ? Regards, Christian ----------------------------------------------------------------- Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Oct 31 06:19:43 2000 Received: from alfmail.cii.fc.ul.pt (alfmail.cii.fc.ul.pt [194.117.6.6]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA21565 for ; Tue, 31 Oct 2000 06:19:38 -0500 Received: from alf1.cii.fc.ul.pt (alf1 [194.117.6.1]) by alfmail.cii.fc.ul.pt (8.11.1/8.11.1) with ESMTP id e9VBIxg03677 for ; Tue, 31 Oct 2000 11:18:59 GMT Received: from localhost (rguedes@localhost) by alf1.cii.fc.ul.pt (8.11.0/8.11.0) with ESMTP id e9VBEfH54342 for ; Tue, 31 Oct 2000 11:14:41 GMT Date: Tue, 31 Oct 2000 11:14:41 +0000 (WET) From: Rita Cardoso Guedes To: CHEMISTRY@ccl.net Subject: benzene dimer Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, can anyone give me some informations about the structure of the benzene dimer and about potential models for benzene ? I will be very grateful Rita From chemistry-request@server.ccl.net Tue Oct 31 07:29:41 2000 Received: from arha.ciens.ula.ve (root@arha.ciens.ula.ve [150.185.128.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA22734 for ; Tue, 31 Oct 2000 07:29:34 -0500 Received: from leviatan (leviatan.ciens.ula.ve [150.185.129.254]) by arha.ciens.ula.ve (8.9.1a/8.9.1) with ESMTP id IAA02113 for ; Tue, 31 Oct 2000 08:23:03 -0400 (GMT-0400) Date: Tue, 31 Oct 2000 08:34:26 -0400 (GMT) From: Javier Eduardo Cuervo Sanchez X-Sender: jcuervo@leviatan To: chemistry@ccl.net Subject: Linda,Gaussian, pgcc and pgf77 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello: We have adquired an evaluation license of Linda for Linux to probe Gaussian 98 in parallel in a cluster beowulf machine. We have compiled and ran the tests in $LINDA/common/cl-examples and $LINDA/common/fl-examples using the compilers of GNU and all works were O.K.! Gaussian 98 must be compiled with Portland Group's compilers (pgcc and pgf77), the compilation is O.K. but when we trying to probe the parallel test of gaussian 98, its have problems (don't finalize). Equal ocurr when we trying to run the different tests in $LINDA/common/cl-example and $LINDA_PATH/common/fl-examples using pgcc and pgf77, we have some problems. We have compiled and ran the different tests (employing pgcc and pgf77) using this configuration: 1.) Set the next environment variables to: setenv LINDA_CC pgcc setenv LINDA_CC_LINK pgcc setenv POSTCPP_CC pgcc setenv LINDA_FORTRAN pgf77 setenv POSTFL_FORTRAN pgf77 setenv LINDA_FORTRAN_LINK pgf77 2.) Recompiled the cmain.o and fmain.o modules in $LINDA_PATH/lib (If we not recompiled this modules the examples can't be compiled succefully) The results obtained (compiling and running the examples) the linda examples were: 1.) In the directory fl-examples (Fortran): a. Compiling: O.K.! b. Running: exited abnormally: [modim@chama1 fl-examples]$ ntsnet fping ntsnet: using executable file /temporal/modim/Pruebas/fl-examples/fping ntsnet: trying to schedule 3 workers ntsnet: scheduled a total of 3 workers ntsnet: starting master process on chama1.ula.edu.ve ntsnet: starting 1 worker on chama2.ula.edu.ve ntsnet: starting 1 worker on chama3.ula.edu.ve ntsnet: starting 1 worker on chama4.ula.edu.ve Floating exception ntsnet: master process exited with signal 11 Floating exception Floating exception Pollable event occured [modim@chama1 fl-examples]$ ntsnet fhello ntsnet: using executable file /temporal/modim/Pruebas/fl-examples/fhello ntsnet: trying to schedule 3 workers ntsnet: scheduled a total of 3 workers ntsnet: starting master process on chama1.ula.edu.ve ntsnet: starting 1 worker on chama2.ula.edu.ve ntsnet: starting 1 worker on chama3.ula.edu.ve ntsnet: starting 1 worker on chama4.ula.edu.ve Floating exception ntsnet: master process exited with signal 11 Floating exception Floating exception Pollable event occured 2.) On the another hand, in cl-examples (C): a. Compiling: Errors: /usr/local/sca/linda-5.0rh6.0/linux-2.2/bin/clc -g -o fastloop fastloop.cl clc (V5.0 Network) PGC-W-0251-Extraneous tokens ignored following # directive (__lt12027.c: 15) .... PGC-W-0251-Extraneous tokens ignored following # directive (__lt12027.c: 643) PGC-S-0035-Syntax error: Recovery attempted by replacing identifier __const by t ypedef id .Z0000 (/usr/include/libio.h: 271) PGC-W-0114-More than one type specified (/usr/include/libio.h: 271) PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: 124) PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: 126) PGC-S-0035-Syntax error: Recovery attempted by replacing identifier __const by t ypedef id .Z0001 (/usr/include/stdio.h: 126) .... Please, Could you help me to configure correctly linda and gaussian 98 with pgcc and pgf77 ? Thanks in Advance, Javier Cuervo CeCalCULA From chemistry-request@server.ccl.net Tue Oct 31 07:47:46 2000 Received: from mailrelay2.lrz-muenchen.de (mailrelay2.lrz-muenchen.de [129.187.254.102]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA22857 for ; Tue, 31 Oct 2000 07:47:43 -0500 Received: from olymp.cup.uni-muenchen.de by mailrelay2.lrz-muenchen.de; Tue, 31 Oct 2000 13:47:28 +0100 Received: by olymp.cup.uni-muenchen.de (AIX 3.2/UCB 5.64/4.03) id AA17172; Tue, 31 Oct 2000 13:47:22 +0100 Date: Tue, 31 Oct 2000 13:47:22 +0100 (MET) From: Stefan Seidler To: chemistry@ccl.net, xmao@iris.sipp.ac.cn Subject: Re: where to get CPMD Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII > Hello, everyone: > I read an article about modeling enzyme mechanism using CPMD, I am > interested in that program, can anyone tell me where I can get it. Try Codes | CPMD http://www.mpi-stuttgart.mpg.de/PARRINELLO/ Regards, Stefan mailto:Stefan.Seidler@cup.uni-muenchen.de From chemistry-request@server.ccl.net Tue Oct 31 02:53:57 2000 Received: from web1702.mail.yahoo.com (web1702.mail.yahoo.com [128.11.23.213]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA20626 for ; Tue, 31 Oct 2000 02:53:56 -0500 Message-ID: <20001031075348.19257.qmail@web1702.mail.yahoo.com> Received: from [161.142.4.9] by web1702.mail.yahoo.com; Mon, 30 Oct 2000 23:53:48 PST Date: Mon, 30 Oct 2000 23:53:48 -0800 (PST) From: sohail qamar Subject: hello ccl friends To: chemistry@ccl.net Cc: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii hello friends! Any reliable software for the generation of 3-D coordinates (NADH)other than Hyperchem and corina. with best wishes to all CCL users, sohail. university sains malaysia. __________________________________________________ Do You Yahoo!? Yahoo! Messenger - Talk while you surf! It's FREE. http://im.yahoo.com/ From chemistry-request@server.ccl.net Tue Oct 31 10:37:13 2000 Received: from sinata.fis.usb.ve (root@sinata.fis.usb.ve [159.90.161.13]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA23870 for ; Tue, 31 Oct 2000 10:37:10 -0500 Received: from fis.usb.ve (papaoso [159.90.161.34]) by sinata.fis.usb.ve (8.9.3/8.9.3-mlv-05-05-2000) with ESMTP id LAA12613 for ; Tue, 31 Oct 2000 11:38:09 -0400 Message-ID: <39FEE313.2B86EADB@fis.usb.ve> Date: Tue, 31 Oct 2000 11:19:48 -0400 From: Hermann Albrecht X-Mailer: Mozilla 4.61 [en] (WinNT; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: CCL: Chemical Applications of Natanzon Potentials Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear all CLL netters: I am an undergraduate chemistry student at the Universidad Simón Bolívar in Caracas, Venezuela. I am currently finishing my Thesis where my tutor and I developed an algebraic method to calculate both bound and scattering states for the Natanzon's Hypergeometric Potentials using a particular representation of the SO(2,1) Lie group. We exemplified our procedure solving the Pöschl-Teller, Rosen-Morse, Eckart and Scarf Potentials. I am currently searching for appropriate bibliography to illustrate the applications in Chemistry of these potentials. Never the less, it has been a difficult task, since Natanzon's Confluent Potentials (i.e. Morse Potential) are more widely used than the Hypergeometric ones. I would like to know if there is any material relating the mentioned potentials to applications in Chemistry, i.e. molecular modeling, description of molecular vibration, spectroscopy and others. I would highly appreciate any information you may send me, since this is the last step to finish the writing of my thesis. Sincerely, Hermann Albrecht halbrech@fis.usb.ve From chemistry-request@server.ccl.net Tue Oct 31 11:25:34 2000 Received: from nottingham.ac.uk (pat.ccc.nottingham.ac.uk [128.243.40.194]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA24245 for ; Tue, 31 Oct 2000 11:25:31 -0500 Received: from gotham.ccc.nottingham.ac.uk ([128.243.40.48] helo=unix.ccc.nottingham.ac.uk) by nottingham.ac.uk with esmtp (Exim 3.13 #2) id 13qeDU-000552-00 for chemistry@ccl.net; Tue, 31 Oct 2000 16:24:52 +0000 Received: from granby ([128.243.40.43] helo=granby.ccc.nottingham.ac.uk) by unix.ccc.nottingham.ac.uk with esmtp (Exim 3.11 #2) id 13qeDn-0007Kk-00 for chemistry@ccl.net; Tue, 31 Oct 2000 16:25:11 +0000 Date: Tue, 31 Oct 2000 16:25:11 +0000 (GMT) From: Simon Cross X-Sender: pcxsc@granby.ccc.nottingham.ac.uk To: ccl list Subject: Spartan Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone used Spartan 5.0 for torsion driving? There is an energy penalty function called sigma that is set to 100 (kcal/mol??) by default - does anyone know about this? It seems a bit excessive when a C-C bond is about 3 kcal/mol. When set to 0 it seems to give a sensible result, but I would like to double check before I run months of dynamics from this system! Cheers, ----------------------------------------- Simon Cross School of Chemistry University of Nottingham tel. 0115 9514193 Email: pcxsc@nottingham.ac.uk From chemistry-request@server.ccl.net Tue Oct 31 11:51:04 2000 Received: from smtp10.atl.mindspring.net (smtp10.atl.mindspring.net [207.69.200.246]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA24369 for ; Tue, 31 Oct 2000 11:51:03 -0500 Received: from quantum (sdn-ar-002ohdaytP192.dialsprint.net [168.191.29.232]) by smtp10.atl.mindspring.net (8.9.3/8.8.5) with ESMTP id LAB26399 for ; Tue, 31 Oct 2000 11:50:48 -0500 (EST) From: "Kevin Gross" To: "CCL" Subject: Atoms in Molecules code Date: Tue, 31 Oct 2000 11:56:20 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Hi all, I've just started learning about Bader's Atoms in Molecules analysis of wavefunctions and it looks quite interesting. I would like to use his freely available code, AIMPAC, but I am at a loss in getting it to run. I have access to an intel linux box. The AIMPAC code I downloaded from his site did not come with a Makefile or even directions regarding the compilation of the source code. Being a novice at compiling programs, I would sure appreciate guidance from someone who has gotten this code working. I did try searching the CCL archives, but couldn't find anything relevant to compiling AIMPAC. I also came across some stuff regarding PROAIM. Is this a different and/or better implementation of the Atoms in Molecules analysis? If so, where would I find this? I will summarize my results. Many thanks, Kevin Gross From chemistry-request@server.ccl.net Tue Oct 31 17:28:21 2000 Received: from ns2.carb.nist.gov (ns2.carb.nist.gov [129.6.112.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA26353 for ; Tue, 31 Oct 2000 17:28:15 -0500 Received: from umbi.umd.edu (hatter.carb.nist.gov [129.6.113.76]) by ns2.carb.nist.gov (8.9.3/8.9.3) with ESMTP id RAA05350 for ; Tue, 31 Oct 2000 17:28:04 -0500 Message-ID: <39FF4789.B52C0E56@umbi.umd.edu> Date: Tue, 31 Oct 2000 17:28:25 -0500 From: "Michael K. Gilson" X-Mailer: Mozilla 4.72 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: MMFF and proteins Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I'm curious about the performance of Merck Molecular Force Field for proteins. Have there been an MD simulations with this? Is there an appropriate water model (e.g., TIP4P) for use with MMFF? Thanks, Mike From chemistry-request@server.ccl.net Tue Oct 31 13:23:24 2000 Received: from jaguar.it.wsu.edu (root@jaguar.it.wsu.edu [134.121.0.73]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA24858 for ; Tue, 31 Oct 2000 13:23:23 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id KAA22593; Tue, 31 Oct 2000 10:20:11 -0800 (PST) Message-ID: <003601c04367$339d1940$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: "Javier Eduardo Cuervo Sanchez" , References: Subject: Re: CCL:Linda,Gaussian, pgcc and pgf77 Date: Tue, 31 Oct 2000 10:20:09 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01C04324.25723820" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 This is a multi-part message in MIME format. ------=_NextPart_000_0033_01C04324.25723820 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi, WARNING! This is a lengthy email filled mostly with examples of what to = "EXACTLY" type into certain files in RedHat6.2. I apologize for the = length in advance! Let me tell you what I have found to work for me with the whole = G98-LINDA-LINUX combintaion: in the file "/etc/profile" make sure you have the following appended: #### export LINDA_PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/ export LINDA_FORTRAN=3Dpgf77 export LINDA_FORTRAN_LINK=3Dpgf77 export POSTFL_FORTRAN=3Dpgf77 export PATH=3D/usr/sca/linda-5.0rh6.0:$PATH export PATH=3D/usr/sca/linda-5.0rh6.0/common/bin:$PATH export PATH=3D/usr/sca/linda-5.0rh6.0/common/lib:$PATH export PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/bin:$PATH export PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/lib:$PATH #### in the file "/etc/hosts.equiv" make sure you have your nodes defined = (example): #### onea.chem.wsu.edu oneb.chem.wsu.edu onec.chem.wsu.edu oned.chem.wsu.edu #### in your "$HOME/.rhosts" file make sure you have your nodes and user = defined: #### onea.chem.wsu.edu administrator oneb.chem.wsu.edu administrator onec.chem.wsu.edu administrator oned.chem.wsu.edu administrator #### in your "$HOME/.cshrc" file append the following: #### g98root=3D/usr gr=3D$HOME if [ "$g98root" ] then gr=3D$g98root fi GAUSS_EXEDIR=3D"$gr/g98/bsd:$gr/g98/private:$gr/g98" GAUSS_ARCHDIR=3D"$gr/g98/arch" GMAIN=3D$GAUSS_EXEDIR PATH=3D$PATH:$GAUSS_EXEDIR LD_LIBRARY_PATH=3D$GAUSS_EXEDIR export GAUSS_EXEDIR GAUSS_ARCHDIR PATH GMAIN LD_LIBRARY_PATH G98BASIS=3D"$gr/g98/basis" ; export G98BASIS #### in your file "$HOME/.bashrc" append the following: #### g98root=3D/usr export g98root PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/lib:$PATH PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/bin:$PATH PATH=3D/usr/sca/linda-5.0rh6.0/common/lib:$PATH PATH=3D/usr/sca/linda-5.0rh6.0/common/bin:$PATH gr=3D$HOME if [ "$g98root" ] then gr=3D$g98root fi GAUSS_EXEDIR=3D"$gr/g98/bsd:$gr/g98/private:$gr/g98" GAUSS_ARCHDIR=3D"$gr/g98/arch" GMAIN=3D$GAUSS_EXEDIR PATH=3D$PATH:$GAUSS_EXEDIR LD_LIBRARY_PATH=3D$GAUSS_EXEDIR export GAUSS_EXEDIR GAUSS_ARCHDIR PATH GMAIN LD_LIBRARY_PATH G98BASIS=3D"$gr/g98/basis" ; export G98BASIS LINDA_FORTRAN=3Dpgf77 export LINDA_FORTRAN LINDA_FORTRAN_LINK=3Dpgf77 export LINDA_FORTRAN_LINK POSTFL_FORTRAN=3Dpgf77 export POSTFL_FORTRAN #### After a quick reboot, you are now ready ready to for some fun. Assuming = you have a standard installation of g98 in /usr and you have a typical = unaltered installation of LINDA in /usr/sca then remove just the fmain.o = file (as SU): #### rm -fv /usr/sca/linda-5.0rh6.0/linux-2.2/lib/fmain.o chmod -v a+rwx /usr/sca/linda-5.0rh6.0/linux-2.2/lib chmod -vR a+rw /usr/sca/linda-5.0rh6.0/common/lib #### Now, run the following #### cd /usr/sca/linda-5.0rh6.0/linux-2.2/lib/ pgf77 -c fmain.f cd $g98root/g98 make -f bsd/g98.make linda #### Assuming you have set up your "tsnet.nodes" file you should now be able = to run G98L. This routine is an agglomeration of a years worth of advice collected = >from Gaussian support help, RedHat forums and SCA technical support. It = works for me, I can't guarentee it twill work for you. Also, do not be = too suprised if some of the stuff above is not necassary. This solution = is far from elegant, and I basically stopped tweaking it once I finally = got it to work! Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message -----=20 From: "Javier Eduardo Cuervo Sanchez" To: Sent: Tuesday, October 31, 2000 4:34 AM Subject: CCL:Linda,Gaussian, pgcc and pgf77=20 >=20 >=20 >=20 > Hello: >=20 > We have adquired an evaluation license of Linda for Linux to probe > Gaussian 98 in parallel in a cluster beowulf machine. >=20 > We have compiled and ran the tests in $LINDA/common/cl-examples and=20 > $LINDA/common/fl-examples using the compilers of GNU and all works = were O.K.! >=20 > Gaussian 98 must be compiled with Portland Group's > compilers (pgcc and pgf77), the compilation is O.K. but when we trying = to > probe the parallel test of gaussian 98, its have problems (don't = finalize). > Equal ocurr when we trying to run the different tests in=20 > $LINDA/common/cl-example and $LINDA_PATH/common/fl-examples using pgcc = and=20 > pgf77, we have some problems. >=20 >=20 > We have compiled and ran the different tests (employing pgcc and = pgf77) using=20 > this configuration: =20 >=20 >=20 > 1.) Set the next environment variables to: > setenv LINDA_CC pgcc > setenv LINDA_CC_LINK pgcc > setenv POSTCPP_CC pgcc > setenv LINDA_FORTRAN pgf77 > setenv POSTFL_FORTRAN pgf77 > setenv LINDA_FORTRAN_LINK pgf77 >=20 > 2.) Recompiled the cmain.o and fmain.o modules in $LINDA_PATH/lib > (If we not recompiled this modules the examples can't be compiled = succefully) >=20 >=20 > The results obtained (compiling and running the examples) the linda = examples=20 > were: >=20 > 1.) In the directory fl-examples (Fortran): > a. Compiling: O.K.! > b. Running: exited abnormally: > [modim@chama1 fl-examples]$ ntsnet fping > ntsnet: using executable file = /temporal/modim/Pruebas/fl-examples/fping > ntsnet: trying to schedule 3 workers > ntsnet: scheduled a total of 3 workers > ntsnet: starting master process on chama1.ula.edu.ve > ntsnet: starting 1 worker on chama2.ula.edu.ve > ntsnet: starting 1 worker on chama3.ula.edu.ve > ntsnet: starting 1 worker on chama4.ula.edu.ve > Floating exception > ntsnet: master process exited with signal 11 > Floating exception > Floating exception > Pollable event occured >=20 > [modim@chama1 fl-examples]$ ntsnet fhello > ntsnet: using executable file = /temporal/modim/Pruebas/fl-examples/fhello > ntsnet: trying to schedule 3 workers > ntsnet: scheduled a total of 3 workers > ntsnet: starting master process on chama1.ula.edu.ve > ntsnet: starting 1 worker on chama2.ula.edu.ve > ntsnet: starting 1 worker on chama3.ula.edu.ve > ntsnet: starting 1 worker on chama4.ula.edu.ve > Floating exception > ntsnet: master process exited with signal 11 > Floating exception > Floating exception > Pollable event occured >=20 >=20 > 2.) On the another hand, in cl-examples (C): > a. Compiling: Errors:=20 > /usr/local/sca/linda-5.0rh6.0/linux-2.2/bin/clc -g -o fastloop = fastloop.cl > clc (V5.0 Network) > PGC-W-0251-Extraneous tokens ignored following # directive = (__lt12027.c: 15) > >.... > PGC-W-0251-Extraneous tokens ignored following # directive = (__lt12027.c: 643) > PGC-S-0035-Syntax error: Recovery attempted by replacing identifier = __const by t > ypedef id .Z0000 (/usr/include/libio.h: 271) > PGC-W-0114-More than one type specified (/usr/include/libio.h: 271) > PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: 124) > PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: 126) > PGC-S-0035-Syntax error: Recovery attempted by replacing identifier = __const by t > ypedef id .Z0001 (/usr/include/stdio.h: 126) > >.... >=20 > Please, Could you help me to configure correctly linda and gaussian 98 = with > pgcc and pgf77 ? >=20 > Thanks in Advance, >=20 >=20 > Javier Cuervo > CeCalCULA >=20 >=20 > -=3D This is automatically added to each message by mailing script = =3D- > 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 >=20 >=20 >=20 >=20 >=20 ------=_NextPart_000_0033_01C04324.25723820 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi,

WARNING!  This is a = lengthy email=20 filled mostly with examples of what to "EXACTLY" type into = certain files in=20 RedHat6.2.  I apologize for the length in advance!
 
Let me tell you what I have found to = work for me=20 with the whole G98-LINDA-LINUX combintaion:

in the=20 file "/etc/profile" make sure you have the following=20 appended:
####
export=20 LINDA_PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/
export=20 LINDA_FORTRAN=3Dpgf77
export LINDA_FORTRAN_LINK=3Dpgf77
export=20 POSTFL_FORTRAN=3Dpgf77
export = PATH=3D/usr/sca/linda-5.0rh6.0:$PATH
export=20 PATH=3D/usr/sca/linda-5.0rh6.0/common/bin:$PATH
export=20 PATH=3D/usr/sca/linda-5.0rh6.0/common/lib:$PATH
export=20 PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/bin:$PATH
export=20 PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/lib:$PATH
####

in the file "/etc/hosts.equiv" make sure you have your = nodes defined=20 (example):
####
onea.chem.wsu.edu
oneb.chem.wsu.edu
onec.chem.wsu.edu
oned.chem.wsu.edu
####
 
in your "$HOME/.rhosts" file make sure = you have=20 your nodes and user defined:
####
onea.chem.wsu.edu = administrator
oneb.chem.wsu.edu = administrator
onec.chem.wsu.edu = administrator
oned.chem.wsu.edu = administrator
####

in your=20 "$HOME/.cshrc" file append the following:
####
g98root=3D/usr
gr=3D$HOME
if [ "$g98root" ]
then gr=3D$g98root
fi
GAUSS_EXEDIR=3D"$gr/g98/bsd:$gr/g98/private:$gr/g98"
GAUSS_ARCHDIR=3D"$gr/g98/arch"
GMAIN=3D$GAUSS_EXEDIR
PATH=3D$PATH:$GAUSS_EXEDIR
LD_LIBRARY_PATH=3D$GAUSS_EXEDIR
export GAUSS_EXEDIR GAUSS_ARCHDIR PATH = GMAIN=20 LD_LIBRARY_PATH
G98BASIS=3D"$gr/g98/basis" ; export=20 G98BASIS
####
 
in your file "$HOME/.bashrc" append the = following:
####
g98root=3D/usr
export g98root
PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/lib:$PATH
PATH=3D/usr/sca/linda-5.0rh6.0/linux-2.2/bin:$PATH
PATH=3D/usr/sca/linda-5.0rh6.0/common/lib:$PATH
=
PATH=3D/usr/sca/linda-5.0rh6.0/common/bin:$PATH
=
gr=3D$HOME
if [ "$g98root" ]
then gr=3D$g98root
fi
GAUSS_EXEDIR=3D"$gr/g98/bsd:$gr/g98/private:$gr/g98"<= /DIV>
GAUSS_ARCHDIR=3D"$gr/g98/arch"
GMAIN=3D$GAUSS_EXEDIR
PATH=3D$PATH:$GAUSS_EXEDIR
LD_LIBRARY_PATH=3D$GAUSS_EXEDIR
export GAUSS_EXEDIR GAUSS_ARCHDIR PATH GMAIN=20 LD_LIBRARY_PATH
G98BASIS=3D"$gr/g98/basis" ; export = G98BASIS
LINDA_FORTRAN=3Dpgf77
export LINDA_FORTRAN
LINDA_FORTRAN_LINK=3Dpgf77
export LINDA_FORTRAN_LINK
POSTFL_FORTRAN=3Dpgf77
export POSTFL_FORTRAN
####
 
 
After a quick reboot, you are now ready = ready to=20 for some fun.  Assuming you have a standard installation of g98 in = /usr and=20 you have a typical unaltered installation of LINDA in /usr/sca then = remove just=20 the fmain.o file (as SU):
####
rm -fv=20 /usr/sca/linda-5.0rh6.0/linux-2.2/lib/fmain.o
chmod -v a+rwx=20 /usr/sca/linda-5.0rh6.0/linux-2.2/lib
chmod -vR a+rw=20 /usr/sca/linda-5.0rh6.0/common/lib
####
 
Now, run the following
 
####
cd = /usr/sca/linda-5.0rh6.0/linux-2.2/lib/
pgf77 -c fmain.f
cd $g98root/g98
make -f bsd/g98.make linda
####
 
Assuming you have set up your "tsnet.nodes" file = you=20 should now be able to run G98L.
 
This routine is an agglomeration of a = years worth=20 of advice collected from Gaussian support help, RedHat forums and SCA = technical=20 support.  It works for me, I can't guarentee it twill work for = you. =20 Also, do not be too suprised if some of the stuff above is not = necassary. =20 This solution is far from elegant, and I basically stopped tweaking it = once I=20 finally got it to work!
 
Respectfully,
Phillip Matz
matz@wsunix.wsu.edu
 

----- Original Message = -----
From:=20 "Javier Eduardo Cuervo Sanchez" <jcuervo@ciens.ula.ve>
To:=20 <chemistry@ccl.net>
Sent: Tuesday, October 31, 2000 4:34 = AM
Subject:=20 CCL:Linda,Gaussian, pgcc and pgf77


>
>
> =
>=20 Hello:
>
> We have adquired an evaluation license of Linda = for=20 Linux to probe
> Gaussian 98 in parallel in a cluster beowulf=20 machine.
>
> We have compiled and ran the tests in=20 $LINDA/common/cl-examples and
> $LINDA/common/fl-examples using = the=20 compilers of GNU and all works were O.K.!
>
> Gaussian 98 = must be=20 compiled with Portland Group's
> compilers (pgcc and pgf77), the=20 compilation is O.K. but when we trying to
> probe the parallel = test of=20 gaussian 98, its have problems (don't finalize).
> Equal ocurr = when we=20 trying to run the different tests in
> $LINDA/common/cl-example = and=20 $LINDA_PATH/common/fl-examples using pgcc and
> pgf77, we have = some=20 problems.
>
>
> We have compiled and ran the = different tests=20 (employing pgcc and pgf77) using
> this configuration:  =
>=20
>
> 1.) Set the next environment variables=20 to:
>     setenv LINDA_CC=20 pgcc
>     setenv LINDA_CC_LINK=20 pgcc
>     setenv POSTCPP_CC=20 pgcc
>     setenv LINDA_FORTRAN=20 pgf77
>     setenv POSTFL_FORTRAN=20 pgf77
>     setenv LINDA_FORTRAN_LINK = pgf77
>=20
> 2.) Recompiled the cmain.o and fmain.o modules in=20 $LINDA_PATH/lib
>    (If we not recompiled this = modules the=20 examples can't be compiled succefully)
>
>
> The = results=20 obtained (compiling and running the examples) the linda examples =
>=20 were:
>
> 1.) In the directory fl-examples=20 (Fortran):
>     a. Compiling:=20 O.K.!
>     b. Running: exited=20 abnormally:
>      [modim@chama1 = fl-examples]$=20 ntsnet fping
>      ntsnet: using = executable file=20 /temporal/modim/Pruebas/fl-examples/fping
>    =  =20 ntsnet: trying to schedule 3 = workers
>     =20 ntsnet: scheduled a total of 3 = workers
>     =20 ntsnet: starting master process on=20 chama1.ula.edu.ve
>      ntsnet: starting = 1=20 worker on chama2.ula.edu.ve
>      = ntsnet:=20 starting 1 worker on = chama3.ula.edu.ve
>     =20 ntsnet: starting 1 worker on=20 chama4.ula.edu.ve
>      Floating=20 exception
>      ntsnet: master process = exited=20 with signal 11
>      Floating=20 exception
>      Floating=20 exception
>      Pollable event = occured
>=20
>      [modim@chama1 fl-examples]$ = ntsnet=20 fhello
>      ntsnet: using executable = file=20 /temporal/modim/Pruebas/fl-examples/fhello
>    = ; =20 ntsnet: trying to schedule 3 = workers
>     =20 ntsnet: scheduled a total of 3 = workers
>     =20 ntsnet: starting master process on=20 chama1.ula.edu.ve
>      ntsnet: starting = 1=20 worker on chama2.ula.edu.ve
>      = ntsnet:=20 starting 1 worker on = chama3.ula.edu.ve
>     =20 ntsnet: starting 1 worker on=20 chama4.ula.edu.ve
>      Floating=20 exception
>      ntsnet: master process = exited=20 with signal 11
>      Floating=20 exception
>      Floating=20 exception
>      Pollable event = occured
>=20
>
> 2.) On the another hand, in cl-examples=20 (C):
>     a. Compiling: Errors:
>=20 /usr/local/sca/linda-5.0rh6.0/linux-2.2/bin/clc -g -o fastloop=20 fastloop.cl
> clc (V5.0 Network)
> PGC-W-0251-Extraneous = tokens=20 ignored following # directive (__lt12027.c: 15)
> >....
> = PGC-W-0251-Extraneous tokens ignored following # directive (__lt12027.c: = 643)
> PGC-S-0035-Syntax error: Recovery attempted by replacing = identifier=20 __const by t
> ypedef id .Z0000 (/usr/include/libio.h: = 271)
>=20 PGC-W-0114-More than one type specified (/usr/include/libio.h: = 271)
>=20 PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: = 124)
>=20 PGC-S-0040-Illegal use of symbol, __const (/usr/include/stdio.h: = 126)
>=20 PGC-S-0035-Syntax error: Recovery attempted by replacing identifier = __const by=20 t
> ypedef id .Z0001 (/usr/include/stdio.h: 126)
> = >....
>=20
> Please, Could you help me to configure correctly linda and = gaussian 98=20 with
> pgcc and pgf77 ?
>
> Thanks in = Advance,
>=20
>
> Javier Cuervo
> CeCalCULA
>
> =
> -=3D=20 This is automatically added to each message by mailing script = =3D-
>=20 CHEMISTRY@ccl.net -- To Everybody    |  =20 CHEMISTRY-REQUEST@ccl.net -- To Admins
> MAILSERV@ccl.net -- HELP=20 CHEMISTRY or HELP SEARCH
> CHEMISTRY-SEARCH@ccl.net -- archive=20 search    |    Gopher: gopher.ccl.net = 70
>=20 Ftp: ftp.ccl.net  |  WWW: = http://www.ccl.net/chemistry/   |=20 Jan: jkl@ccl.net
>
>
>
>
>=20
------=_NextPart_000_0033_01C04324.25723820-- From chemistry-request@server.ccl.net Tue Oct 31 17:49:38 2000 Received: from mb2i0.ns.pitt.edu (mb2i0.ns.pitt.edu [136.142.186.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA26460 for ; Tue, 31 Oct 2000 17:49:37 -0500 Received: from recife ("port 1915"@[136.142.153.159]) by pitt.edu (PMDF V5.2-32 #41462) with SMTP id <01JVZUT6MYSC00FO87@mb2i0.ns.pitt.edu> for chemistry@ccl.net; Tue, 31 Oct 2000 17:48:49 EST Date: Tue, 31 Oct 2000 17:59:13 -0500 From: Gustavo Moura Subject: Semiempirical Magnetic Moments To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: 7bit Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Dear CCL readers, I am looking for material (papers, books, WebPages?, etc) describing the semiempirical (CNDO and/or INDO) evaluation of magnetic moment integrals. I already found material describing the semiempirical calculation of electric dipole moments and now I need material describing the evaluation of magnetic moment integrals. I am also interested in knowing about the origin dependence of such semiempirical integrals and how to solve it (are there semiempirical GIAOs?). Thank you very much in advance. Sincerely yours, Gustavo L.C. Moura gustavo@dumbo.chem.pitt.edu From chemistry-request@server.ccl.net Tue Oct 31 12:19:34 2000 Received: from eddings.acpub.duke.edu (eddings.acpub.duke.edu [152.3.233.76]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id MAA24606 for ; Tue, 31 Oct 2000 12:19:34 -0500 Received: from ZhenyuLu (dhcp9141.chem.duke.edu [152.3.169.141]) by eddings.acpub.duke.edu (8.9.3/8.9.3/Duke-5.0.0) with SMTP id MAA08942; Tue, 31 Oct 2000 12:19:21 -0500 (EST) Message-ID: <003901c0435e$a5a4c640$8da90398@chem.duke.edu> From: "Zhenyu Lu" To: Subject: molecular mechanic paramters for neutralized residues Date: Tue, 31 Oct 2000 12:18:54 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0036_01C04334.BC594020" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_0036_01C04334.BC594020 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCL folks: I am trying QM/MM calculations on a enzyme. We are interested in the electrostatic role of the enzyme enviroment. Instead of using counter ions, we just neutralized most Lys, Arg, Glu, Asp redsidues to see what will happen. I am using Tinker program, and the paramter files (Amber, Charmm,etc) don't accomordate=20 these neutralized residues.=20 My quetion is : Where or is there some way that I can obtain the parameters for the neutralized Lys, Arg, Glu, Asp residues? Help on how to simulate the true system, using counter ions, = protonation state exploration,etc. is also appreciated. Thanks in advance! Best, Zhenyu Lu Duke University =20 ------=_NextPart_000_0036_01C04334.BC594020 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear CCL folks:
 
I am trying QM/MM calculations on = a enzyme.  We=20 are interested
in the electrostatic role of the enzyme = enviroment.=20 Instead of using
counter ions, we just neutralized  most Lys, = Arg, Glu,=20 Asp redsidues
to see what will happen. I am using Tinker program, = and=20 the
paramter files (Amber, Charmm,etc) don't accomordate =
these neutralized residues.
My quetion is :
Where or is there some  way that I can obtain = the=20 parameters
for the neutralized Lys, Arg, Glu, Asp = residues?
 
Help on how to simulate the true system,=20 using  counter ions, protonation
state exploration,etc. is also = appreciated.
 
Thanks in advance!
Best,
Zhenyu Lu
Duke University
 
 
------=_NextPart_000_0036_01C04334.BC594020--