From chemistry-request@server.ccl.net Thu May 2 06:50:43 2002 Received: from web21301.mail.yahoo.com ([216.136.173.212]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g42Aoh109921 for ; Thu, 2 May 2002 06:50:43 -0400 Message-ID: <20020502105033.34871.qmail@web21301.mail.yahoo.com> Received: from [195.29.54.82] by web21301.mail.yahoo.com via HTTP; Thu, 02 May 2002 11:50:33 BST Date: Thu, 2 May 2002 11:50:33 +0100 (BST) From: =?iso-8859-1?q?Wolfgang=20Rebecus?= Subject: Compile Gaussian98 on MPI To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLs, I would like to know how to compile Gaussian 98 with MPI on two (or more) different machines (Intel PIII with different speed). Can someone suggest me is that possible and perhaps some good reference to start (which include exactly all the steps that one must do, where to find MPI, maybe some public script or something’s like that available...) Thanks, W. Rebecus __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page > from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Thu May 2 01:49:45 2002 Received: from red.CACheSoftware.com (IDENT:root@[12.17.172.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g425nh101178 for ; Thu, 2 May 2002 01:49:44 -0400 Received: from daveg-lifebook.cachesoftware.com ([192.168.110.100]) by red.CACheSoftware.com (8.11.6/8.9.3/3) with ESMTP id g4209GF01883; Wed, 1 May 2002 17:09:16 -0700 Message-Id: <5.1.0.14.0.20020501180209.029380c0@pop3.norton.antivirus> X-Sender: daveg/mail.cachesoftware.com@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Wed, 01 May 2002 18:11:06 -0700 To: chemistry@ccl.net From: David Gallagher Subject: Re: Mopac with Cygwin Cc: David Case In-Reply-To: <20020501104939.A455581@gamow.scripps.edu> References: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed The latest version of MOPAC 2002 runs under Linux and Windows. It is not free but it is fully supported by Fujitsu. For technical information see http://www.cachesoftware.com/techsupport/mopac/ David Gallagher, Fujitsu At 10:49 AM 5/1/2002 -0700, David Case wrote: >On Mon, Apr 29, 2002, Stephen Bowlus wrote: > > > I am trying to run Mopac 6 on a P3/Win2K machine under Cygwin. Set up for > > 20 heavy/30 light atoms and without ESP, the program compiles with g77 with > > only 2 small complaints. Test runs invoked by redirection (mopac < input > > > output) end with a segmentation fault. The stackdump gives an error > about a > > status access violation. > > > >In my experience, such problems are not limited to Cygwin: I have had >similar experience with a number of mopac's (versions 5,6,and 7) on Linux, >IRIX, and other Unix systems. > >The only free (as in beer) version I have seen that seems to work reliably >with "modern" Unix and Unix-like systems is from the Minnesota group: > > http://comp.chem.umn.edu/mopac > >However, this version is provided under a license agreement that doesn't >permit redistribution. > >Let me emphasize that I am *not* a mopac expert, and I have not spent time >trying to debug any of the codes I have tried. I would be delighted to hear > > from the CCL community of pointers to other mopac's that work well under >Linux/cygwin, particularly those that could be freely redistributed. > > >...thanks...dac > >-- > >================================================================== >David A. Case | e-mail: case@scripps.edu >Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 >The Scripps Research Institute | phone: +1-858-784-9768 >10550 N. Torrey Pines Rd. | home page: >La Jolla CA 92037 USA | http://www.scripps.edu/case >================================================================== > > >-= 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 ============================================== David A. Gallagher, C. Chem. Vice President, Sales and Marketing CAChe Group Fujitsu America, Inc. 15244 NW Greenbrier Parkway Beaverton, OR 97006-5733, USA Direct dial: 503 746 3607 Main Switchboard: 503 746 3600 Fax: 503 531 9966 email: dgallagher@cachesoftware.com URL: http://www.cachesoftware.com ============================================== From chemistry-request@server.ccl.net Thu May 2 06:24:25 2002 Received: from mail.fqspl.com.pl ([212.244.147.20]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g42AON109327 for ; Thu, 2 May 2002 06:24:24 -0400 Received: (qmail 6914 invoked by uid 505); 2 May 2002 10:24:54 -0000 Received: from victor@fqspl.com.pl by mail by uid 502 with qmail-scanner-1.10 (F-PROT: 3.11. Clear:0. Processed in 0.803551 secs); 02 May 2002 10:24:54 -0000 Received: from unknown (HELO test) (213.76.41.104) by mail.fqspl.com.pl with SMTP; 2 May 2002 10:24:53 -0000 Message-ID: <000c01c1f1c3$d22a7880$68294cd5@test> From: "Victor Anisimov" To: "David Case" , References: <20020501104939.A455581@gamow.scripps.edu> Subject: Re: CCL:Mopac with Cygwin Date: Thu, 2 May 2002 12:24:08 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit 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 ----- Original Message ----- From: "David Case" To: Sent: Wednesday, May 01, 2002 7:49 PM Subject: CCL:Mopac with Cygwin > On Mon, Apr 29, 2002, Stephen Bowlus wrote: > > > I am trying to run Mopac 6 on a P3/Win2K machine under Cygwin. Set up for > > 20 heavy/30 light atoms and without ESP, the program compiles with g77 with > > only 2 small complaints. Test runs invoked by redirection (mopac < input > > > output) end with a segmentation fault. The stackdump gives an error about a > > status access violation. > > > > In my experience, such problems are not limited to Cygwin: I have had > similar experience with a number of mopac's (versions 5,6,and 7) on Linux, > IRIX, and other Unix systems. > > Just my few cents: Try Compaq Fortran on Windows and PGI Fortran compiler on Linux. This will make any version of MOPAC working. Best regards, Victor. Victor Anisimov, PhD Senior Software Researcher - Computational Chemist FQS Poland, Fujitsu ul. Starowislna 13-15, 31-038 Krakow, Poland Email: victor@fqspl.com.pl Tel.(+48 12) 429-4345 Fax(+48 12) 429-6124 From chemistry-request@server.ccl.net Thu May 2 08:56:13 2002 Received: from cclh41.chm.tu-dresden.de ([141.30.198.41]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42CuC112346 for ; Thu, 2 May 2002 08:56:12 -0400 Received: from cclh41 (localhost [127.0.0.1]) by cclh41.chm.tu-dresden.de (8.11.3/8.11.3/SuSE Linux 8.11.1-0.5) with SMTP id g42CsfA15214 for ; Thu, 2 May 2002 14:54:41 +0200 Content-Type: text/plain; charset="iso-8859-1" From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de Organization: TU Dresden To: chemistry@ccl.net Subject: Re: CCL:Mopac with Cygwin Date: Thu, 2 May 2002 14:54:41 +0200 X-Mailer: KMail [version 1.2] References: <20020501104939.A455581@gamow.scripps.edu> <000c01c1f1c3$d22a7880$68294cd5@test> In-Reply-To: <000c01c1f1c3$d22a7880$68294cd5@test> MIME-Version: 1.0 Message-Id: <02050214544101.13598@cclh41> Content-Transfer-Encoding: 8bit On Thursday 02 May 2002 12:24, you wrote: > Just my few cents: > Try Compaq Fortran on Windows and PGI Fortran compiler on Linux. > This will make any version of MOPAC working. This is not true. I was never able to compile MOPAC97 with PGI fortran. Also my question on CCL many months (or years ?) ago doesn't solve this. Matthias -- Dr. Matthias Mann Fachrichtung Chemie, TU Dresden, D-01062 Dresden Tel.: +49 (351) 463-34286 / Fax: -33162 Email: Matthias.Mann@chemie.tu-dresden.de From chemistry-request@server.ccl.net Thu May 2 14:40:14 2002 Received: from scsx01.sc.ehu.es (root@[158.227.150.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42IeBI01385 for ; Thu, 2 May 2002 14:40:14 -0400 Received: from sq.ehu.es (sqpx31.sq.ehu.es [158.227.161.31]) by scsx01.sc.ehu.es (8.9.3/8.9.1) with ESMTP id RAA00872 for ; Thu, 2 May 2002 17:03:39 +0200 (MET DST) Message-ID: <3CD15562.4090507@sq.ehu.es> Date: Thu, 02 May 2002 17:04:02 +0200 From: Txema Mercero Reply-To: pobmelat@sq.ehu.es User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@server.ccl.net Subject: Freq Calculation with Gaussian Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi there, I am Performing a Freq calculation for a molecule with 23 atoms, C2v symmetry, and 467 basis set. The problem is that it seems it is not going to finish ever .... , it is in the following step: ------------------------------------------------------- Differentiating once with respect to nuclear coordinates. Integrals replicated using symmetry in FoFDir. MinBra= 0 MaxBra= 3 Meth= 1. IRaf= 0 NMat= 12 IRICut= 12 DoRegI=T DoRafI=T ISym2E= 2 JSym2E=2. There are 24 degrees of freedom in the 1st order CPHF. 24 vectors were produced by pass 0. AX will form 12 AO Fock derivatives at one time. 24 vectors were produced by pass 1. 24 vectors were produced by pass 2. 24 vectors were produced by pass 3. ..... 1 vectors were produced by pass213. 1 vectors were produced by pass214. 1 vectors were produced by pass215. --------------------------------------------------------------- I have been using Gaussian fo a while an I have never seen a claculation of these type taking soo long. Does anybody have an explanation or similar experience? Txema Mercero Euskal Herriko Unibertsitatea From chemistry-request@server.ccl.net Thu May 2 14:23:49 2002 Received: from mr.usu.edu ([129.123.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42INmI01049 for ; Thu, 2 May 2002 14:23:48 -0400 Received: from tapaskar (tapaskar.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 3536E1E9F2 for ; Thu, 2 May 2002 12:23:41 -0600 (MDT) Reply-To: From: "Tapas Kar" To: Subject: Non convergence in SCF calculation (GAMESS program) Date: Thu, 2 May 2002 12:21:47 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000E_01C1F1D3.EDC3F340" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_000E_01C1F1D3.EDC3F340 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Hi: I got SCF convergence problem in Gamess. It looks energy is oscillating. Is there any option in gamess to manage the convergence problem? Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - "The value of pi was first calculated by Budhayana, and he explained the concept of what is now known as the Pythagorean Theorem. British scholars have last year (1999) officially published that Budhayan’s works dates to the 6th Century, which is long before the European mathematicians." ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu ------=_NextPart_000_000E_01C1F1D3.EDC3F340 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi:=20
I got SCF=20 convergence problem in Gamess. It looks energy is=20 oscillating.
Is there=20 any option in gamess to manage the convergence = problem?
Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein -
"The value = of pi was=20 first calculated by Budhayana, and he explained
the concept of what = is now=20 known as the Pythagorean Theorem. British
scholars have last year = (1999)=20 officially published that Budhayan=92s
works dates to the 6th = Century, which is=20 long before the=20 European
mathematicians."
----------------------------------= ----------------------------------------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email:=20 tapaskar@cc.usu.edu
      =20 tapas@risky3.chem.usu.edu

 
------=_NextPart_000_000E_01C1F1D3.EDC3F340-- From chemistry-request@server.ccl.net Thu May 2 14:18:42 2002 Received: from rrzd1.rz.uni-regensburg.de (root@[132.199.1.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42IIcI00898 for ; Thu, 2 May 2002 14:18:42 -0400 Received: from listserv.ngate.uni-regensburg.de (kroesus2.rz.uni-regensburg.de [132.199.2.208]) by rrzd1.rz.uni-regensburg.de (8.9.3/8.9.3-KLW-Linux-0.1) with ESMTP id RAA07695 for ; Thu, 2 May 2002 17:44:09 +0200 Received: from KROESUS2/SpoolDir by listserv.ngate.uni-regensburg.de (Mercury 1.48); 2 May 02 17:44:08 +0200 Received: from SpoolDir by KROESUS2 (Mercury 1.48); 2 May 02 17:44:03 +0200 From: "Georg Schmeer" Organization: Universitaet Regensburg To: chemistry@ccl.net Date: Thu, 2 May 2002 17:43:58 +0200 MIME-Version: 1.0 Content-type: text/plain; charset=ISO-8859-1 Subject: Compiling g98 A11 with ATLAS Message-ID: <3CD17ADC.27869.12627C8@localhost> Priority: normal X-mailer: Pegasus Mail for Win32 (v3.12c) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from Quoted-printable to 8bit by server.ccl.net id g42IIgI00903 Dear G98-users, I need some help for the compiling of gaussian98 Rev.A11. I got Gaussian98 Rev.A11 from Gaussian,Inc on one CD containing two directories. One directory contains the gaussian98 Rev.A11 tar file and the other the tar file of the ATLAS-linear algebra system and also blas- and f77blas-libraries for IBM AIX-Systems. After dearchiving the two tar-files I compiled the ATLAS-library according to the appropriate instructions on a Pentium III processor under Suse- LINUX 7.2. The compilers are gcc and PGF90. After a rather long time the compilation finished without error messages and produced 7 libraries in the directory ATLAS/lib/Linux_PIIISSE1_2: libatlas.a libcblas.a libf77blas.a liblapack.a libptcblas.a libptf77blas.a libtstatlas.a In order to compile g98 I copied these libraries in the directory $g98root/g98/lib and made the following modifications in the file g98.make: BLAS = $g98root/g98/lib/libatlas.a \ $g98root/g98/lib/libcblas.a \ $g98root/g98/lib/libf77blas.a \ $g98root/g98/lib/liblapack.a \ $g98root/g98/lib/libptcblas.a \ $g98root/g98/lib/libptf77blas.a \ $g98root/g98/lib/libtstatlas.a The compilation of g98 via "bsd/bldg98 >& bldg98.log &" stops shortly before the end with the following lines in bldg98.log: . . if ( 1 ) then . . make[1]: Leaving directory `&g98root/g98´ pgf90 -O2 -tp p6 -Munroll -Mvect=cachesize:524288 -o g98 ml0.o util.so util.so: undefined reference to `atl_f77wrap_dspmv_´ util.so: undefined reference to `atl_f77wrap_dgemm_´ make: *** [g98] Error 1 endif The error message is the same when compiling with pgf77. In the directory ATLAS/interfaces/blas/F77/src/f77wrap I found the generic routines atl_F77wrap_gemm.c and atl_F77wrap_spmv.c but no hint for the double-precison routines respectively. The Gaussian 98 Release Notes Revisions A.11.2 and A.11.3 give instructions for Fortran Compiler and Libraries for Building the Intel Linux Version on page 14, these instructions are useless, however, since the appropriate libraries are lacking. Therefore any help to locate the error which I made, would be appreciated. Is there any people familiar with compiling of gaussian98 together with ATLAS? Sincerely yours Georg Schmeer Prof. Dr. Georg Schmeer Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg Georg.Schmeer@chemie.uni-regensburg.de Tel: 0941-943-4745 Fax: 0941-943-1690 From chemistry-request@server.ccl.net Thu May 2 09:15:05 2002 Received: from Laterita.ismm.edu.cu ([65.169.240.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42DEU112753 for ; Thu, 2 May 2002 09:14:56 -0400 Received: (from daemon@localhost) by Laterita.ismm.edu.cu (8.11.2/8.11.2) id g42DJCe29122 for chemistry@ccl.net.AVP; Thu, 2 May 2002 09:19:12 -0400 Received: (from daemon@localhost) by Laterita.ismm.edu.cu (8.11.2/8.11.2) id g42DJC029110 for ; Thu, 2 May 2002 09:19:12 -0400 Received: from UNKNOWN(172.16.5.6), claiming to be "correo.ismmm.edu.cu" via SMTP by Laterita, id smtpdBFMiLy; Thu May 2 09:19:07 2002 Received: by correo.ismmm.edu.cu with Internet Mail Service (5.5.2653.19) id ; Thu, 2 May 2002 09:14:27 -0400 Message-ID: <31C4AA55DDF46240AB3229310BCCD05B1928A3@correo.ismmm.edu.cu> From: Alexis Otero Calvi To: "'chemistry@ccl.net'" Subject: G98: Convergence failure Date: Thu, 2 May 2002 09:14:26 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C1F1DB.48ED07F0" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C1F1DB.48ED07F0 Content-Type: text/plain Hello all, I am calculating a system with Ni, P, O and H atoms. I am using a LANL2DZ basis set for Ni and 6-31G(d) for P, O and H. How I can solve this problem. (Convergence failure). ***************************************** of initial guess= 0.7500 Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Virtual orbitals will be shifted by 0.100 hartree. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. Restarting both DIIS and incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(UB+HF-LYP) = -1131.49839249 A.U. after 65 cycles Convg = 0.5771D-04 -V/T = 2.0581 S**2 = 0.7697 Annihilation of the first spin contaminant: S**2 before annihilation 0.7697, after 0.7501 Convergence failure -- run terminated. Error termination via Lnk1e in d:\aotero\g98w\l502.exe. Job cpu time: 0 days 2 hours 56 minutes 56.0 seconds. File lengths (MBytes): RWF= 24 Int= 0 D2E= 0 Chk= 1 Scr= 1 I would greatly appreciate any help. Alexis ------_=_NextPart_001_01C1F1DB.48ED07F0 Content-Type: text/html Content-Transfer-Encoding: quoted-printable Mensaje

Hello = all,

I am calculating a = system with Ni, P, O and H atoms. I am using a LANL2DZ basis set for Ni and = 6-31G(d) for P, O and H.

 

How I can solve this problem. (Convergence failure).

 

 

*****************************************<= o:p>

<S**2> of = initial guess=3D 0.7500

 Requested convergence on RMS = density matrix=3D1.00D-08 within  = 64 cycles.

 Requested convergence on MAX = density matrix=3D1.00D-06.

 Virtual orbitals will be = shifted by   0.100 = hartree.

 Restarting both DIIS and = incremental Fock formation.

 Restarting both DIIS and = incremental Fock formation.

 Restarting both DIIS and = incremental Fock formation.

 >>>>>>>>= >> Convergence criterion not met.

 SCF Done:  E(UB+HF-LYP) =3D  -1131.49839249     A.U. = after   65 = cycles

       &nb= sp;     Convg  =3D    0.5771D-04       &nb= sp;     -V/T =3D  = 2.0581

       &nb= sp;     S**2   = =3D   = 0.7697

 Annihilation of the first spin contaminant:

 S**2 before annihilation     0.7697,   after     = 0.7501

 Convergence failure -- run = terminated.

 Error termination via Lnk1e in = d:\aotero\g98w\l502.exe.

 Job cpu time:  0 days  2 hours 56 = minutes 56.0 seconds.

 File lengths (MBytes):  RWF=3D   24 Int=3D    0 D2E=3D    0 Chk=3D    1 Scr=3D    = 1

 

 

 

I would greatly = appreciate any help.

 

Alexis

 

 

 

 

------_=_NextPart_001_01C1F1DB.48ED07F0-- From chemistry-request@server.ccl.net Thu May 2 08:51:51 2002 Received: from vytautas.vdu.lt ([193.219.38.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42Cpo112248 for ; Thu, 2 May 2002 08:51:51 -0400 Received: from vaidila.vdu.lt ([193.219.38.52] ident=mail) by vytautas.vdu.lt with esmtp for chemistry@ccl.net id 173G3k-0002Tq-00; Thu, 02 May 2002 14:51:44 +0200 Received: from vejas.vdu.lt ([193.219.38.82] helo=TYREX) by vaidila.vdu.lt with esmtp for chemistry@ccl.net id 173G5P-0004W5-00; Thu, 02 May 2002 14:53:27 +0200 Date: Thu, 2 May 2002 15:51:43 +0300 From: a3arzi X-Mailer: The Bat! (v1.44) UNREG / CD5BF9353B3B7091 Reply-To: "Art'" X-Priority: 3 (Normal) Message-ID: <10814189423.20020502155143@vaidila.vdu.lt> To: chemistry@ccl.net Subject: CCL: scoring functions Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello CCL'ers, Question about where get some free/commercial good scoring function to evaluate docking results. Any suggestions are welcome. -- Best regards, Arturas Z. mailto:a3arzi@vaidila.vdu.lt http://biologija.vdu.lt/person/ziemar/index.html From chemistry-request@server.ccl.net Thu May 2 15:07:47 2002 Received: from mailer.gwdg.de ([134.76.10.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42J7lI03228 for ; Thu, 2 May 2002 15:07:47 -0400 Received: from vrlab03.mpibpc.gwdg.de ([134.76.211.99] helo=mpi-bpc.mpg.de) by mailer.gwdg.de with esmtp (Exim 3.33 #11) id 173LvX-0005hW-00; Thu, 02 May 2002 21:07:39 +0200 Message-ID: <3CD18E74.2020002@mpi-bpc.mpg.de> Date: Thu, 02 May 2002 21:07:32 +0200 From: Vlad Cojocaru User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4) Gecko/20011126 Netscape6/6.2.1 X-Accept-Language: en-us MIME-Version: 1.0 To: CCL list , amber list Subject: new RNA residues Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit I have created new residues ready for introducing them in RNA. The approach was the following: -I created the residue starting with one already existing (ex: 2amino purine starting from adenine) -I derived the missing parameters using antechamber from Amber7. -The charges were derived using two stage RESP fit. -The residues were them introduced in a simple AMber minimizer in vacuum using an igb=3(distance dependent) and a dielectric constant equal to 4. I have 2 questions: -The total energy obtained from the minimization is positive. What is the significance of such values for the total energy? -Does anyone tried this kind of an approach and if yes can anybody give me some ideeas how to prove the consistency of the models that I have created? How could I prove that they are correct? I have already received some answers to this matter and I want to thank for all. Best regards, vlad -- Vlad Cojocaru Max Planck Institut for Biophysical Chemistry Deparment: 060 Am Fassberg 11, 37077 Goettingen, Germany tel: ++49-551-201.1389 e-mail: Vlad.Cojocaru@mpi-bpc.mpg.de From chemistry-request@server.ccl.net Thu May 2 18:02:51 2002 Received: from mail.rochester.edu (root@[128.151.224.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g42M2pI09236 for ; Thu, 2 May 2002 18:02:51 -0400 Received: from there (ice.chem.rochester.edu [128.151.195.5]) by mail.rochester.edu (8.12.1/8.12.1) with SMTP id g42M29Rw6381812; Thu, 2 May 2002 18:02:09 -0400 (EDT) Message-Id: <200205022202.g42M29Rw6381812@mail.rochester.edu> Content-Type: text/plain; charset="us-ascii" From: weizhuang Reply-To: weiz@mail.rochester.edu To: ponder@dasher.wustl.edu Subject: help Date: Thu, 2 May 2002 18:20:10 -0400 X-Mailer: KMail [version 1.3.1] Cc: CHEMISTRY@ccl.net, weiz@mail.rochester.edu MIME-Version: 1.0 Content-Transfer-Encoding: 8bit X-Filter-Version: 1.7 (mail1) Dear Sir: I met some problems here. I am using tinker.I want to do MD to a system with 32 CH2(OH)CH(OH)CH2(OH) molecules( this is a preconditioning of the solvent which I want to use in a ab initio MD simulation). first I create a molecule, then I use "xyzedit" to create a periodic box (15.87A for each side) and fill in the 32 molecules. then I wrote the key file. it is: -------------------------------- ARCHIVE EWALD A-AXIS 15.87 ALPHA 90.0 THERMOSTAT ANDERSEN parameters mm3.prm ----------------------------- then I use "newton" to optimize the system ( by the way, it didn't reach a 0.01 GMS but a "SMALLfct" what is it?) then I run "dynamic". but it seems a terriblly huge calculation because after 1 hour the monitor is still idle. and when I took off the "A-AXIS 15.87 ALPHA 90.0" keywords and then run the dynamic. the system just "fly off"( it is natual because it is a isolated system) so could you please tell me what is wrong with my operations above?