From sxr224@anugpo.anu.edu.au Mon May 20 02:54:07 1996 Received: from anugpo.anu.edu.au for sxr224@anugpo.anu.edu.au by www.ccl.net (8.7.1/950822.1) id CAA10487; Mon, 20 May 1996 02:35:49 -0400 (EDT) Received: from surya.anu.edu.au (surya.anu.edu.au [150.203.193.135]) by anugpo.anu.edu.au (8.6.12/8.6.12) with SMTP id QAA02185 for ; Mon, 20 May 1996 16:35:42 +1000 Message-Id: <199605200635.QAA02185@anugpo.anu.edu.au> Comments: Authenticated sender is From: "Shoba Ranganathan" To: chemistry@www.ccl.net Date: Mon, 20 May 1996 16:16:46 +0000 Subject: Re: Strychnine Coordinates Reply-to: Shoba.Ranganathan@anu.edu.au Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Dear Pablo, } } I send you as an attached file the crystallographic coordinates for } strychnine. They are taken from the CSD database (.dat file format, } sorry but I cannot transform to PDB or xyz). Two sets of coordinates } are present in the file: at room T and 130 K. } } I hope this helps. } } Pablo } } -------------------------------------------------------------------- } Pablo Vitoria Garcia Departamento de Quimica Inorganica, } Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado } 644, E-48080 Bilbao SPAIN Phone: +34 4 4647700 Ext. 2450 } -------------------------------------------------------------------- Thanks for the coordinates - these were a great help. Regards Shoba PS: mail to qipvigap@lg.ehu.es is bouncing back to me - hence the post to CCL. =========================================================== Dr. Shoba RANGANATHAN Computational Mol Biology & Drug Design Group Div. of Biochemistry & Mol. Biology John Curtin School of Medical Research Australian National University Tel: +616-279-8301 Canberra ACT 0200 Fax: +616-249-0415 Australia. email:Shoba.Ranganathan@anu.edu.au ===========(http://biocomp.anu.edu.au/~sra/)============== From wallenborn@phys.chem.ethz.ch Mon May 20 04:54:08 1996 Received: from bernina.ethz.ch for wallenborn@phys.chem.ethz.ch by www.ccl.net (8.7.1/950822.1) id EAA13868; Mon, 20 May 1996 04:26:16 -0400 (EDT) Received: from helios (actually helios-chem.ethz.ch) by bernina.ethz.ch with SMTP inbound; Mon, 20 May 1996 10:25:34 +0200 Received: from jetson by helios.ethz.ch id AA17262; Mon, 20 May 1996 10:25:32 +0200 Sender: wall@phys.chem.ethz.ch Message-Id: <31A02C7D.4584@phys.chem.ethz.ch> Date: Mon, 20 May 1996 10:25:33 +0200 From: Ernst Wallenborn Organization: ETH Zuerich X-Mailer: Mozilla 2.0 (X11; I; SunOS 5.4 sun4m) Mime-Version: 1.0 To: chemistry@www.ccl.net Subject: [Q] G94 Excited States X-Url: http://www.ccl.net/ccl/welcome.html#3 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi there, i need to calculate an electronic spectrum of an aromatic compound (yes it was my boss' idea, yes i did tell him that this is much easier to measure and no fun to calculate, no he didn't find my opinion useful and constructive). Now the problem is: the thing is far too big for US-GAMESS (USG has no direct CI, hence it's not expensive to calculate, it's plain impossible with our HD configuration), it is too big for a reasonable CAS in g94 (i have a Pi space of 20 orbitals, of which at least ten have to be included) CIS on the other hand takes (STO-3g, this was a test) about 30 minutes on my SPARC 2, but it's results are, well, not overwhelming. So the question is: Is there any possibility of doing anything better than CIS but cheaper than CAS in g94? In GAMESS i'd do a CISD versus CISD(T) calculation in the style of Shavitt's 70's calculation of the acetone spectrum, but as i mentioned, i think US-GAMESS is likely to fail. I tried #3-21g* casscf(10,10,nroot=1) iop(4/17=10,4/18=10,4/19=1) where the 4/19 option should have set up a FOCI MCSCF (in GAMESS language), but ended up with a eof error on stdin. After checking the programmer's manual i added 64 1 1 1 2 3 4 5 1 2 3 4 5 to the .com, where 64 is the number of occupied orbitals, and 1 2 3 4 5 1 2 3 4 5 the reference configuration. That gave me lots of TAPE READ ERRORs. Besides a test run on water showed a difference between 4/19=2 and GAMESS MCSCF SOCI=.T., so they are not identical anyway. Any help? -- -ernst wallenborn. i'm not a bug. i'm an undocumented feature. From csilmt12@area.BA.CNR.IT Mon May 20 10:54:15 1996 Received: from icnucevx.cnuce.cnr.it for csilmt12@area.BA.CNR.IT by www.ccl.net (8.7.1/950822.1) id KAA19522; Mon, 20 May 1996 10:12:17 -0400 (EDT) Received: from area.ba.cnr.it by mailsrv.cnuce.cnr.it (PMDF V5.0-6 #9955) id <01I4XNUB6N66A8CWGI@mailsrv.cnuce.cnr.it> for chemistry@www.ccl.net; Mon, 20 May 1996 16:11:32 +0100 (MET) Received: by area.ba.cnr.it; (5.65/1.1.8.2/27Mar96-1138AM) id AA04302; Mon, 20 May 1996 16:11:21 +0200 Date: Mon, 20 May 1996 16:11:21 +0200 (MET DST) From: Massimo Trotta Subject: autoprotolysis constant of alcohols To: chemistry@www.ccl.net Message-id: <9605201411.AA04302@area.ba.cnr.it> MIME-version: 1.0 X-Mailer: ELM [version 2.4 PL24 PGP3 *ALPHA*] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7bit dear all, I am trying to find out the constant of autoprotolysis of alcohols: the equilibrium constant for the reaction of alcohols in which and ROH molecules accepts a H+ from another ROH molecules. This is equivalent to the ionic product of water. Has anybody an idea where to find these values or how to evaluate them? any help will be useful. NB eventually will summrize. massimo -- !==============================================================! ! Massimo Trotta ! ! Centro Studi Chimico Fisici sull'Interazione Luce Materia ! ! c/o Dept. of Chemistry ! ! V. Orabona, 4 I-70126 Italy ! ! e-mail: csilmt12@area.ba.cnr.it ! ! http://www.ba.cnr.it/~csilmt12 !==============================================================! From rochus@felix.anorg.chemie.tu-muenchen.de Mon May 20 11:54:13 1996 Received: from felix.anorg.chemie.tu-muenchen.de for rochus@felix.anorg.chemie.tu-muenchen.de by www.ccl.net (8.7.1/950822.1) id LAA19952; Mon, 20 May 1996 11:11:15 -0400 (EDT) Received: by felix.anorg.chemie.tu-muenchen.de (940816.SGI.8.6.9/930416.SGI) for chemistry@www.ccl.net id RAA28320; Mon, 20 May 1996 17:11:07 +0200 From: "Rochus Schmid" Message-Id: <9605201711.ZM28318@felix> Date: Mon, 20 May 1996 17:11:07 -0600 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: benzene box Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear Netters, In adition to my recent question concerning cff91/benzene: Does anyone of you have an equilibrated box of benzene molecules (in any format)? Thanks in advance, Rochus -- ******************************************************************************** Rochus Schmid Technische Universitaet Muenchen Tel. ++49 89 3209 3140 Anorganisch Chemisches Institut 1 Fax. ++49 89 3209 3473 Prof. W. A. Herrmann E-mail: Lichtenbergstrasse 4 rochus@felix.anorg.chemie.tu-muenchen.de 85747 Garching ******************************************************************************** From vam@kon.icp.ac.ru Mon May 20 11:57:42 1996 Received: from kon.icp.ac.ru for vam@kon.icp.ac.ru by www.ccl.net (8.7.1/950822.1) id LAA20086; Mon, 20 May 1996 11:31:11 -0400 (EDT) Received: (vam@localhost) by kon.icp.ac.ru (8.6.12/8.6.5) id UAA05218 for chemistry@www.ccl.net; Sun, 19 May 1996 20:15:18 +0400 Date: Sun, 19 May 1996 20:15:18 +0400 From: Victor Anisimov Message-Id: <199605191615.UAA05218@kon.icp.ac.ru> To: chemistry@www.ccl.net Subject: MOPAC-93 memory requirements Dear netters, Does someone have experience compiling MOPAC-93 for big dimensions, 100x100, 200x200 heavy and light atoms, for example. How much virtual space they will reqire? I'm getting "can't allocate memory" message on FreeBSD with 400Mbyte of virtual space on hard disk for 100x100 one. What is this, low virtual space or Fortran compiler error, does someone know? Thanks for any idea. Victor. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ *** Institute of Chemical Physics in Chernogolovka *** * Russian Academy of Sciences * * * * Dr. Victor M. Anisimov * *** vam@kon.icp.ac.ru *** ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ From Jeffrey.Nauss@UC.EDU Mon May 20 13:54:13 1996 Received: from jazz.san.uc.edu for Jeffrey.Nauss@UC.EDU by www.ccl.net (8.7.1/950822.1) id NAA20978; Mon, 20 May 1996 13:45:17 -0400 (EDT) Received: from ucmod2.che.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #7238) id <01I4XIOD07BCD6GQRR@UCBEH.SAN.UC.EDU>; Mon, 20 May 1996 13:43:08 -0500 (EST) Received: from ucmod2.che.uc.edu by ucmod2.che.uc.edu via SMTP (951211.SGI.8.6.12.PATCH1042/951211.SGI.AUTO) id NAA12368; Mon, 20 May 1996 13:43:31 -0400 Date: Mon, 20 May 1996 13:43:15 -0400 From: "Jeffrey L. Nauss" Subject: Heating before Molecular Dynamics - Summary Sender: nauss@UC.EDU Cc: chemistry@www.ccl.net, DIBUG@sunsite.icm.edu.pl Message-id: <31A0AF33.41C6@UC.Edu> Organization: Dept. Chem., University of Cincinnati MIME-version: 1.0 X-Mailer: Mozilla 3.0b3 (X11; I; IRIX 5.3 IP12) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Newsgroups: bionet.molec-model Quite sometime ago, I asked the following question: ======================================================================== From Jeffrey.Nauss@UC.EDU Fri Apr 12 15:04:35 1996 When using CHARMM or AMBER for molecular dynamics, the system is usually heated to the required temperature, ran in an equilibration period, and only then is the actual production run. However, in Discover, there is no heating phase. The system is instanteously heated to the required temperature and equilibrated before the production phase. Why the difference in the two approaches? What is Discover doing differently from CHARMM and AMBER so that a heating phase is not required? ======================================================================== Basically, it appears that the difference lies merely in a philosophical difference in running molecular dynamics simulations. The folks at Biosym (now MSI) felt that instantaneous heating was acceptable if the equilibration period was handled correctly. However, the authors for CHARMM and AMBER felt that a heating period was necessary at all times. Here are edited excerpts from the few responses that I got. If anyone has some references with some hardcore data, I'd appreciate hearing from you. From: zauhar@xhost5.tripos.COM (Randy Zauhar) This is a question of "computing philosophy"... What is the benefit of slow heating? I have seen some argue that overall equilibration time is improved if you use slow heating, rather than "jarring" the system by rapidly increasing the temperature. In my very subjective evaluation, it probably doesn't matter that much. ...the algorithms are indeed different. In the heating method, atom velocities are simply rescaled at set intervals of dynamics steps. In the heat bath method, atomic velocities are rescaled at every step with the velocity scaling controlled by factor whose functional form includes the ratio of current to target temperature, as well as a temperature coupling factor that controls how rapidly the temperature is adjusted toward the target value. From: slickers@imb-jena.de (Peter Slickers) In me opinion it depends on the system you are modelling and not on the software whether an extended heating and equilibration phase is requiered. I have run some MD simulations with DNA in a box of water with counterions and salt with AMBER 4.1. For such a system with several mobile charges you need a carefull and extended heating procedure, otherwise the DNA double helix will disrupt. From: Leif Laaksonen I'm not sure but I see this as a semantic issue. Combining the heating and equilibration into one stage should be no problem. You can more or less assign the atom velocities and scale them directly. I guess CHARMM has an explicit heating stage to prevent "shock" heating by allowing the user to control the speed in which the temperature is raised. -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From bernhold@npac.syr.edu Mon May 20 14:54:13 1996 Received: from postoffice.npac.syr.edu for bernhold@npac.syr.edu by www.ccl.net (8.7.1/950822.1) id NAA21044; Mon, 20 May 1996 13:57:40 -0400 (EDT) Received: from oldnova.npac.syr.edu (bernhold@oldnova.npac.syr.edu [128.230.7.4]) by postoffice.npac.syr.edu (8.7.5/8.7.1) with ESMTP id NAA26111; Mon, 20 May 1996 13:57:36 -0400 (EDT) Received: from localhost (bernhold@localhost) by oldnova.npac.syr.edu (8.7.1/8.7.1) with SMTP id NAA10981; Mon, 20 May 1996 13:57:34 -0400 (EDT) Message-Id: <199605201757.NAA10981@oldnova.npac.syr.edu> X-Authentication-Warning: oldnova.npac.syr.edu: bernhold owned process doing -bs X-Authentication-Warning: oldnova.npac.syr.edu: Host bernhold@localhost didn't use HELO protocol To: Victor Anisimov cc: chemistry@www.ccl.net Subject: Re: CCL:M:MOPAC-93 memory requirements In-reply-to: Message from Victor Anisimov of "Sun, 19 May 1996 20:15:18 +0400." <199605191615.UAA05218@kon.icp.ac.ru> Date: Mon, 20 May 1996 13:57:22 -0400 From: "David E. Bernholdt" I seem to recall that MOPAC 7 compiled for 100 heavy + 100 light atoms took up about 130 MB on an IBM RS/6000. Should be able the same on most other platforms, since most of the space is common blocks, not code. Is it 400 MB _free_ virtual memory, or 400 MB _total_ VM? Depending on what else you're doing on the machine you could have a lot less than 400 free. Also, trying to run very large memory jobs on my RS/6000, I've had problems with jobs that apparently should fit comfortably within the free VM, but not in physical memory. When I get _closer_ to the neighborhood of free physical memory, it works. I haven't had time to sort this out yet, but you could be experiencing something similar. Hope this helps. -- David E. Bernholdt | Email: bernhold@npac.syr.edu Northeast Parallel Architectures Center | Phone: +1 315 443 3857 111 College Place, Syracuse University | Fax: +1 315 443 1973 Syracuse, NY 13244-4100 | URL: http://www.npac.syr.edu From gmercier@helix.nih.gov Mon May 20 16:54:20 1996 Received: from helix.nih.gov for gmercier@helix.nih.gov by www.ccl.net (8.7.1/950822.1) id QAA23181; Mon, 20 May 1996 16:31:41 -0400 (EDT) Received: from [128.231.66.71] (ppc71.od.nih.gov [128.231.66.71]) by helix.nih.gov (8.6.13/8.6.12) with SMTP id QAA21691 for ; Mon, 20 May 1996 16:31:38 -0400 Message-Id: Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Mon, 20 May 1996 16:32:12 -0500 To: chemistry@www.ccl.net From: gmercier@helix.nih.gov (Gustavo A. Mercier, Jr.) Subject: dendrimer builder Hi! A few weeks ago I asked about a dendrimer coordinate builder suitable to generate initial coordinates for MM/MD simulations. I received a few suggestions, and a few requests for the answers. Unfortunately, no builder is currently available, so I went ahead and programmed one taking advantage of the coordinate manipulation features of Charmm. I first must thank those who submitted suggestions, and the support people from MSI who rebuilt my original patch! For the benefit of those who requested it, I am appending the rtf and Charmm script file at the end of this file. The rtf file below supports the necessary patches to construct a PAMAM starburst dendrimer with a NH3 core. If you write your own patches, the Charmm script is "generic" enough that you should be able to construct different starburst dendrimers with a different core, or repeat unit. In a nutshell, the Charmm script below computes the necessary offsets so that the correct indeces in the linear sequence of repeat units (specified by the SEQUENCE command) are used to generate the links that build the dendrimer. The links are generated using the patching mechanism of Charmm. The difficulty with programs that expect a linear polymer like the amino acid sequence of a protein is that making the apropriate links between different residues can be confusing. If anybody is interested in details of the script (ie. reference to the equations, etc.), please e-mail me directly. Finally, some caveats: 1) the rtf is suitable to construct the coordinates. There may be some holes in the description of the internal coordinates that define the force field, ie. an improper dihedral may not be specified etc. 2) the script and the rtf have only been tested under Charmm 23.1 as supplied under Quanta 4.1.1 by MSI, and with an older parm file, PARM22. 3) the amidoamine unit (AMT) is defined in its extended and trans form. 4) it may be appropriate to sequentially build the dendrimer with minimization or dynamic runs relaxing the system as you build successive generations. This will require modifying the script, but this is not too difficult. 5) i don't claim that the algorithm below is the most efficient way of doing this! I am sure some graph theory inclined people can do a much better job! Bye and Good Luck! ******* Charmm script ******* * PAMAM dendrimer coordinate builder * written by Gustavo A. Mercier, Jr. * NIH/LDRR 4/96 * ... Example G=3 * bomb -2 ! UPPER ! read the dendrimer rtf and a parameter file read rtf card name dd.rtf read para card name parm.prm ! Here we define the variables that define the dendrimer set Nc 3 ! Number of branches in the core set Ng 3 ! Number of Generations = 2 set Nb 2 ! Branches at Branchpoint = Nb = 2 ! Here we initialize other variables set NRb 0 ! Total number of Residues in the branch; computed below set Zp 1 ! Branchpoints at the periphery = Zp = 1 set Of1 0 ! Offset1 to move over residues to patch a branchpoint ! Number of residues used up to Ng-2 set Of2 0 ! Offset2 to move over branchpoints ! Number of residues used up to Ng-1 set iNc 1 ! Counter for the number of branches in the core set iNg 1 ! Counter for the generations = g set iNb 1 ! Counter for the branchpoints set iRh 0 ! Residue index of the head = ri ! Here you specify variables for each residue that attaches to the head ! in your patch; We assume that one patch makes all the necessary ! changes at a branchpoint. Otherwise, you would have to loop ! over the patches, and take appropriate care over the indeces of ! the residues; In the PAMAM case the patch DEND uses 2 residues ! as tails to one head. set iRt1 0 ! Residue index of the tail 1 set iRt2 0 ! Residue index of the tail 2 ! Here we initialize storage variables set sto1 0 ! storage set sto2 0 ! storage ! First, generate the three branches ! individually so that the residues of a branch ! are together in the output coordinate file ! Successive branches have segid = # of branch ! Total number of residues in a branch LET sto1 = @Ng + 1 LET sto2 = @Nb ** @sto1 LET sto2 = @sto2 - 1 LET sto1 = @Nb - 1 LET NRb = @sto2 / @sto1 LABEL L_CORE READ SEQU AMT @NRb GENE @iNc SETUP ! patch the branch LABEL L_GEN ! CALC Zp ( @Nb ) ** ( ( @iNg ) - 1 ) LET Zp = @iNg - 1 LET Zp = @Nb ** @Zp ! CALC Of2 ( @Zp - 1 ) / ( @Nb - 1 ) LET sto1 = @Zp - 1 LET sto2 = @Nb - 1 DIVI sto1 BY @sto2 ! This is done to avoid some bug with LET SET Of2 @sto1 ! CALC Of1 ( ( ( @Nb ) * ( @Zp ) ) - 1 ) / ( @Nb - 1 ) LET sto1 = @Nb * @Zp LET sto1 = @sto1 - 1 LET sto2 = @Nb - 1 LET Of1 = @sto1 / @sto2 LABEL L_BRANP ! CALC iRh @Of2 + @iNb LET iRh = @Of2 + @iNb ! CALC iRt1 @Of1 + 1 LET iRt1 = @Of1 + 1 ! CALC iRt2 @Of1 + 2 LET iRt2 = @Of1 + 2 PATCH DEND @iNc @iRh @iNc @iRt1 @iNc @iRt2 SETUP SET Of1 @iRt2 INCR iNb BY 1 IF @iNb GT @Zp THEN GOTO E_BRANP GOTO L_BRANP LABEL E_BRANP SET iNb 1 ! reset the counter INCR iNg BY 1 IF @iNg GT @Ng THEN GOTO E_GEN GOTO L_GEN LABEL E_GEN SET iNg 1 INCR iNc BY 1 IF @iNc GT @Nc THEN GOTO E_CORE GOTO L_CORE LABEL E_CORE ! Now link to the core; here it is NH3 READ SEQU card * NH3 * 1 NH3 GENE 0 SETUP PATCH NGZ 0 1 1 1 2 1 3 1 SETUP ! Now generate the coordinates IC PARA IC SEED 0 1 N 1 1 C1 1 1 C2 IC BUILD IC FILL print ic print coor write coor card name "test.crd" * PAMAM g3 NH3 core * ! You could write a PSF if you wanted to! ! write psf card name "test.PSF" ! * PAMAM g3 NH3 core ! * STOP ******* End of Charmm script ******** ******* Begin rtf ******** * Topology file containing the dendrimer units * ... * ... 4/25/96 Modified by G. Mercier M.D.,Ph.D.. * ... Original by G. Mercier, but DEND patch written * ... by Dr. Funchness of support at msi.com (4/24/96) * ... * sorted alphabetically; metals follow organics * Atom type numbers 201-229 are reserved for special QUANTA display atom types. * Last current active number is 234. * 22 0 MASS 170 AR 39.948 Ar ! Argon MASS 7 B 10.81 B ! Boron MASS 14 C 12.01100 C ! Carbonyl or Guanidinium carbon MASS 190 C3 12.01100 C ! Carbonyl carbon in 3-membered aliphatic ring MASS 192 C4 12.01100 C ! Carbonyl carbons in 4-membered aliphatic ring MASS 21 C5R 12.01100 C ! Aromatic carbon in a five membered ring MASS 23 C5RE 13.01900 C ! Extended aromatic carbon in five membered ring MASS 28 C5RP 12.01100 C ! for Aryl-Aryl bond between C5R rings MASS 189 C5RQ 12.01100 C ! for second Ar-Ar bond between C5RP rings (ortho) MASS 22 C6R 12.01100 C ! Aromatic carbon in a six membered ring MASS 24 C6RE 13.01900 C ! Extended aromatic carbon in six membered ring MASS 29 C6RP 12.01100 C ! for Aryl-Aryl bond between C6R rings MASS 194 C6RQ 12.01100 C ! Carbon of C6RP type ortho to C6RP pair MASS 230 CF1 12.01100 C ! Carbon with one Fluorine MASS 231 CF2 12.01100 C ! Carbon with two Fluorines MASS 232 CF3 12.01100 C ! Carbons with three Fluorines MASS 11 CH1E 13.01900 C ! Extended atom carbon with one hydrogen MASS 12 CH2E 14.02700 C ! Extended atom carbon with two hydrogens MASS 13 CH3E 15.03500 C ! Extended atom carbon with three hydrogens MASS 15 CM 12.01100 C ! Carbonmonoxide, or other triply bonded, carbon MASS 199 CP3 12.01100 C ! Carbon on nitrogen in proline ring MASS 197 CPH1 12.01100 C ! CG and CD2 carbons in histidine ring MASS 198 CPH2 12.01100 C ! CE1 carbon in histidine ring MASS 195 CQ66 12.01100 C ! Third adjacent pair of CR66 types in fused rings MASS 25 CR55 12.01100 C ! Aromatic carbon-merged five membered rings MASS 26 CR56 12.01100 C ! Aromatic carbon-merged five/six membered rings MASS 27 CR66 12.01100 C ! Aromatic carbon-merged six membered rings MASS 196 CS66 12.01100 C ! Second adjacent pair of CR66 types in fused rings MASS 10 CT 12.01100 C ! Aliphatic carbon (tetrahedral) MASS 191 CT3 12.01100 C ! in 3-membered aliphatic ring, usually tetrahedral MASS 193 CT4 12.01100 C ! in 4-membered aliphatic ring, usually tetrahedral MASS 16 CUA1 12.01100 C ! Carbon in double bond, first pair MASS 17 CUA2 12.01100 C ! Carbon in double bond, second conjugated pair MASS 20 CUA3 12.01100 C ! Carbon in double bond, third conjugated pair MASS 18 CUY1 12.01100 C ! Carbon in triple bond, first pair MASS 19 CUY2 12.01100 C ! Carbon in triple bond, second conjugated pair MASS 1 H 1.00800 H ! Hydrogen bonding hydrogen (neutral group) MASS 3 HA 1.00800 H ! Aliphatic or aromatic hydrogen MASS 2 HC 1.00800 H ! Hydrogen bonding hydrogen (charged group) MASS 168 HE 4.00260 He ! Helium MASS 9 HMU 1.00800 H ! Mu-bonded hydrogen for metals and boron-hydride MASS 8 HO 1.00800 H ! Hydrogen on an alcohol oxygen MASS 4 HT 1.00800 H ! TIPS3P water model hydrogen MASS 171 KR 83.80 Kr ! Krypton MASS 5 LP 0.0 ! ST2 lone pair MASS 31 N 14.00670 N ! Nitrogen; planar-valence of 3, i.e. nitrile, etc. MASS 234 N3 14.00670 N ! Nitrogen in a three membered ring MASS 34 N5R 14.00670 N ! Nitrogen in a five membered aromatic ring MASS 30 N5RP 14.00670 N ! for Ar-Ar bond between five membered rings MASS 35 N6R 14.00670 N ! Nitrogen in a six membered aromatic ring MASS 39 N6RP 14.00670 N ! for Aryl-Aryl bond between six membered rings MASS 37 NC 14.00670 N ! Charged guanidinium-type nitrogen MASS 186 NC2 14.00670 N ! for neutral guanidinium group - Arg sidechain MASS 169 NE 20.179 Ne ! Neon MASS 38 NO2 14.00670 N ! Nitrogen in nitro, or related, group MASS 32 NP 14.00670 N ! Nitrogen in peptide, amide, or related, group MASS 183 NR1 14.00670 N ! Protonated nitrogen in neutral histidine ring MASS 184 NR2 14.00670 N ! Unprotonated nitrogen in neutral histidine ring MASS 185 NR3 14.00670 N ! Nitrogens in charged histidine ring MASS 182 NR55 14.00670 N ! N at fused bond between two 5-membered aromatics MASS 180 NR56 14.00670 N ! N at fused bond between 5 and 6-membered aryls MASS 181 NR66 14.00670 N ! N at fused bond between two 6-membered aromatics MASS 36 NT 14.00670 N ! Nitrogen (tetrahedral), i.e. Amine, etc. MASS 33 NX 14.00670 N ! Proline nitrogen, or similar MASS 40 O 15.99940 O ! Carbonyl oxygen for amides, or related structures MASS 56 O2M 15.99940 O ! Oxygen in Si-O-Al or Al-O-Al bond MASS 52 O5R 15.99940 O ! Oxygen in 5 membered aromatic ring-radicals, etc. MASS 53 O6R 15.99940 O ! Oxygen in 6 membered aromatic ring-radicals, etc. MASS 41 OA 15.99940 O ! Carbonyl oxygen for aldehydes, or related MASS 51 OAC 15.99940 O ! Carbonyl oxygen for acids, or related MASS 43 OC 15.99940 O ! Charged oxygen MASS 50 OE 15.99940 O ! Ether oxygen / Acetal oxygen MASS 47 OH2 15.99940 O ! ST2 water model oxygen MASS 42 OK 15.99940 O ! Carbonyl oxygen for ketones, or related MASS 48 OM 15.99940 O ! Carbonmonoxide, or other triply bonded, oxygen MASS 49 OS 15.99940 O ! Ester oxygen MASS 57 OSH 0.00000 O ! Massless O for zeolites, or related cage cmpds. MASS 55 OSI 15.99940 O ! Oxygen in Si-O-Si bond MASS 45 OT 15.99940 O ! Hydroxyl oxygen (tetrahedral) or Ionizable acid MASS 46 OW 15.99940 O ! TIP3P water model oxygen MASS 64 P6R 30.9738 P ! Phosphorous in aromatic 6-membered ring MASS 61 PO3 30.9738 P ! Phosphorous bonded to three oxygens MASS 62 PO4 30.9738 P ! Phosphorous bonded to four oxygens MASS 60 PT 30.9738 P ! Phosphorous, general; usually tetrahedral MASS 63 PUA1 30.9738 P ! Phosphorous double bond MASS 233 PUY1 30.9738 P ! Triple bonded phosphorus MASS 173 RN 222.0 Rn ! Radon MASS 72 S5R 32.0600 S ! Sulphur in a five membered aromatic ring MASS 73 S6R 32.0600 S ! Sulphur in a six membered aromatic ring MASS 74 SE 32.060 S ! Thioether sulphur MASS 71 SH1E 33.06800 S ! Extended atom sulphur with one hydrogen MASS 75 SK 32.060 S ! Thioketone sulphur MASS 76 SO1 32.0600 S ! Sulphur bonded to one oxygen MASS 77 SO2 32.0600 S ! Sulphur bonded to two oxygens MASS 78 SO3 32.0600 S ! Sulphur bonded to three oxygens MASS 79 SO4 32.0600 S ! Sulphur bonded to four oxygens MASS 70 ST 32.06000 S ! Sulphur, general; usually tetrahedral MASS 131 XAT 210.0 At ! Astatine MASS 94 XBR 79.904 Br ! Bromine MASS 93 XCL 35.45300 Cl ! Chlorine MASS 172 XE 131.29 Xe ! Xenon MASS 92 XF 18.99840 F ! Fluorine MASS 95 XI 126.9045 I ! Iodine MASS 126 MAC 227.0278 Ac ! Actinium MASS 111 MAG 107.868 Ag ! Silver MASS 91 MAL 26.9815 Al ! ALuminum MASS 159 MAM 243.0 Am ! Americium MASS 101 MAS 74.9216 As ! Arsenic MASS 119 MAU 196.08 Au ! Gold MASS 115 MBA 137.33 Ba ! Barium MASS 6 MBE 9.01218 Be ! Beryllium MASS 122 MBI 208.9804 Bi ! Bismuth MASS 161 MBK 247.0 Bk ! Berkelium MASS 84 MCA 40.080 Ca ! Calcium MASS 112 MCD 112.41 Cd ! Cadmium MASS 124 MCE 140.12 Ce ! Cerium MASS 162 MCF 251.0 Cf ! Californium MASS 160 MCM 247.0 Cm ! Curium MASS 99 MCO 58.9332 Co ! Cobalt MASS 98 MCR 51.996 Cr ! Chromium MASS 89 MCS 132.9054 Cs ! Cesium MASS 96 MCU 63.546 Cu ! Copper MASS 150 MDY 162.50 Dy ! Dysprosium MASS 152 MER 167.26 Er ! Erbium MASS 163 MES 252.0 Es ! Einsteinium MASS 147 MEU 151.96 Eu ! Europium MASS 86 MFE 55.847 Fe ! Iron MASS 164 MFM 257.0 Fm ! Fermium MASS 142 MFR 223.0 Fr ! Francium MASS 135 MGA 69.72 Ga ! Gallium MASS 148 MGD 157.25 Gd ! Gadolinium MASS 136 MGE 72.59 Ge ! Germanium MASS 175 MHA 262.0 Ha ! Hahnium MASS 138 MHF 178.49 Hf ! Hafnium MASS 120 MHG 200.59 Hg ! Mercury MASS 151 MHO 164.9304 Ho ! Holmium MASS 137 MIN 114.82 In ! Indium MASS 140 MIR 192.22 Ir ! Iridium MASS 83 MK 39.098 K ! Potassium MASS 123 MLA 138.9055 La ! Lanthanum MASS 80 MLI 6.941 Li ! Lithium MASS 167 MLR 260.0 Lr ! Lawrencium MASS 155 MLU 174.967 Lu ! Lutetium MASS 165 MMD 258.0 Md ! Medelevium MASS 82 MMG 24.305 Mg ! Magnesiun MASS 85 MMN 54.938 Mn ! Manganese MASS 107 MMO 95.94 Mo ! Molybdenum MASS 81 MNA 22.9898 Na ! Sodium MASS 106 MNB 92.9064 Nb ! Niobium MASS 144 MND 144.24 Nd ! Neodymium MASS 100 MNI 58.69 Ni ! Nickel MASS 166 MNO 259.0 No ! Nobelium MASS 157 MNP 237.0482 Np ! Neptunium MASS 117 MOS 190.2 Os ! Osmium MASS 156 MPA 231.0359 Pa ! Protactinium MASS 121 MPB 207.2 Pb ! Lead MASS 110 MPD 106.42 Pd ! Palladium MASS 145 MPM 145.0 Pm ! Promethium MASS 130 MPO 209.0 Po ! Polonium MASS 125 MPR 140.9077 Pr ! Praseodymium MASS 118 MPT 195.08 Pt ! Platinum MASS 158 MPU 244.0 Pu ! Plutonium MASS 143 MRA 226.0254 Ra ! Radium MASS 88 MRB 85.4678 Rb ! Rubidium MASS 176 MRE 186.31 Re ! Rhenium MASS 174 MRF 261.0 Rf ! Rutherfordium/Kurchatovium MASS 109 MRH 102.9055 Rh ! Rhodium MASS 108 MRU 101.07 Ru ! Ruthenium MASS 114 MSB 121.75 Sb ! Antimony MASS 133 MSC 44.9559 Sc ! Scandium MASS 102 MSE 78.96 Se ! Selenium MASS 90 MSI 28.0855 Si ! Silicon MASS 177 MSIU 28.08550 Si ! Silicon when as double bond MASS 146 MSM 150.36 Sm ! Samarium MASS 113 MSN 118.69 Sn ! Tin MASS 103 MSR 87.62 Sr ! Strontium MASS 139 MTA 180.9479 Ta ! Tantalum MASS 149 MTB 158.9254 Tb ! Terbium MASS 132 MTC 98.0 Tc ! Technetium MASS 129 MTE 127.60 Te ! Tellurium MASS 127 MTH 232.0381 Th ! Thorium MASS 134 MTI 47.88 Ti ! Titanium MASS 141 MTL 204.383 Tl ! Thallium MASS 153 MTM 168.9342 Tm ! Thulium MASS 128 MU 238.0289 U ! Uranium MASS 97 MV 50.9415 V ! Vanadium MASS 116 MW 183.85 W ! Tungsten MASS 104 MY 88.9059 Y ! Yttrium MASS 154 MYB 173.04 Yb ! Ytterbium MASS 87 MZN 65.38 Zn ! Zinc MASS 105 MZR 91.22 Zr ! Zirconium ! Autogenerate all angles during generation of the PSF ! AUTOGENERATE ANGLES DIHEDRALS ! Apply terminal patches NONE and NONE by default during ! generation of the PSF DEFA FIRS NONE LAST NONE ! ! NH3 RESI NH3 GROUP ATOM N NT -0.30 ATOM H1 H 0.10 ATOM H2 H 0.10 ATOM H3 H 0.10 DONO H1 N DONO H2 N DONO H3 N ACCE N H1 BOND N H1 N H2 N H3 THET H1 N H2 H1 N H3 H2 N H3 IMPH H3 H2 N H1 IC H3 H2 *N H1 0.000 0.0 120.0 0.0 0.00 ! The AMT molecule RESI AMT 0.00 GROUP ATOM C1 CT -0.15 ATOM H1 HA 0.05 ATOM H2 HA 0.05 ATOM H12 HA 0.05 GROUP ATOM C2 CT -0.05 ATOM H3 HA 0.05 ATOM H4 HA 0.05 ATOM C3 C 0.60 ATOM O1 O -0.55 ATOM N1 NP -0.40 ATOM H5 H 0.25 ATOM C4 CT -0.05 ATOM H6 HA 0.05 ATOM H7 HA 0.05 GROUP ATOM C5 CT -0.10 ATOM H8 HA 0.05 ATOM H9 HA 0.05 GROUP ATOM N2 NT -0.30 ATOM H10 H 0.15 ATOM H11 H 0.15 BOND C1 H12 C1 H1 C1 H2 BOND C1 C2 C2 H3 C2 H4 C2 C3 BOND C3 O1 C3 N1 BOND N1 H5 N1 C4 BOND C4 H6 C4 H7 C4 C5 BOND C5 H9 C5 H8 C5 N2 BOND N2 H10 N2 H11 ! IMPH N1 C3 C4 H5 ! my impropers IMPH H1 C2 C1 H2 IMPH H1 C2 C1 H12 IMPH H3 C1 C2 H4 IMPH H3 C1 C2 C3 IMPH O1 C2 C3 N1 IMPH H5 C3 N1 C4 IMPH H6 N1 C4 H7 IMPH H6 N1 C4 C5 IMPH H8 C4 C5 N2 IMPH H8 C4 C5 N2 IMPH H10 C5 N2 H11 ! DONO H5 N1 ACCE O1 C3 IC C1 C2 C3 N1 0.000 0.0 180.0 0.0 0.000 IC C1 C2 C3 O1 0.000 0.0 0.0 0.0 0.000 IC C2 C3 N1 C4 0.000 0.0 180.0 0.0 0.000 IC C3 N1 C4 C5 0.000 0.0 180.0 0.0 0.000 IC N1 C4 C5 N2 0.000 0.0 180.0 0.0 0.000 IC C3 C2 C1 H1 0.000 0.0 60.0 0.0 0.000 IC C3 C2 C1 H2 0.000 0.0 -60.0 0.0 0.000 IC N1 C3 C2 H3 0.000 0.0 60.0 0.0 0.000 IC N1 C3 C2 H4 0.000 0.0 -60.0 0.0 0.000 IC O1 C3 N1 H5 0.000 0.0 180.0 0.0 0.000 IC C3 N1 C4 H6 0.000 0.0 -60.0 0.0 0.000 IC C3 N1 C4 H7 0.000 0.0 60.0 0.0 0.000 IC N1 C4 C5 H8 0.000 0.0 -60.0 0.0 0.000 IC N1 C4 C5 H9 0.000 0.0 60.0 0.0 0.000 IC C4 C5 N2 H10 0.000 0.0 120.0 0.0 0.000 IC C4 C5 N2 H11 0.000 0.0 -120.0 0.0 0.000 IC C3 C2 C1 H12 0.000 0.0 180.0 0.0 0.000 ! Patch to generate the g0 core in ! NH3 core PAMAM ! residue 1 is the NH3 core ! residue 2 is C1 head one ! residue 3 is C1 head two ! residue 4 is C1 head three ! ! 2C1---- ! / ! 1N-----------3C1------- ! \ ! 4C1---- PRES NGZ ATOM 1N NT -0.15 ATOM 2C1 CT -0.05 ATOM 2H1 HA 0.05 ATOM 2H2 HA 0.05 ATOM 3C1 CT -0.05 ATOM 3H1 HA 0.05 ATOM 3H2 HA 0.05 ATOM 4C1 CT -0.05 ATOM 4H1 HA 0.05 ATOM 4H2 HA 0.05 DELE ATOM 1H1 DELE ATOM 1H2 DELE ATOM 1H3 DELE ATOM 2H12 DELE ATOM 3H12 DELE ATOM 4H12 BOND 1N 2C1 1N 3C1 1N 4C1 THET 2C1 1N 3C1 THET 2C1 1N 4C1 THET 3C2 1N 4C1 THET 1N 2C1 2C2 THET 1N 3C1 3C2 THET 1N 4C1 4C2 THET 1N 2C1 2H1 THET 1N 2C1 2H2 THET 1N 3C1 3H1 THET 1N 3C1 3H2 THET 1N 4C1 4H1 THET 1N 4C1 4H2 DIHE 3C1 1N 2C1 2H1 DIHE 3C1 1N 2C1 2H2 DIHE 3C1 1N 2C1 2C2 DIHE 2C1 1N 3C1 3H1 DIHE 2C1 1N 3C1 3H2 DIHE 2C1 1N 3C1 3C2 DIHE 3C1 1N 4C1 4H1 DIHE 3C1 1N 4C1 4H2 DIHE 3C1 1N 4C3 4C2 DIHE 1N 2C1 2C2 2H3 DIHE 1N 2C1 2C2 2H4 DIHE 1N 2C1 2C2 2C3 DIHE 1N 3C1 3C2 3H3 DIHE 1N 3C1 3C2 3H4 DIHE 1N 3C1 3C2 3C3 DIHE 1N 4C1 4C2 4H3 DIHE 1N 4C1 4C2 4H4 DIHE 1N 4C1 4C2 4C3 IMPH 4C1 3C1 1N 2C1 IMPH 2H1 1N 2C1 2H2 IMPH 2H1 1N 2C1 2C2 IMPH 3H1 1N 3C1 3H2 IMPH 3H1 1N 3C1 3C2 IMPH 4H1 1N 4C1 4H2 IMPH 4H1 1N 4C1 4C2 IC 4C1 3C1 *1N 2C1 0.000 0.0 120.0 0.0 0.000 IC 3C1 1N 2C1 2C2 0.000 0.0 -60.0 0.0 0.000 IC 1N 2C1 2C2 2C3 0.000 0.0 180.0 0.0 0.000 IC 2C2 2C1 1N 3C1 0.000 0.0 120.0 0.0 0.000 IC 2C1 1N 3C1 3C2 0.000 0.0 90.0 0.0 0.000 IC 1N 3C1 3C2 3C3 0.000 0.0 180.0 0.0 0.000 IC 2C2 2C1 1N 4C1 0.000 0.0 -120.0 0.0 0.000 IC 2C1 1N 4C1 4C2 0.000 0.0 180.0 0.0 0.000 IC 1N 4C1 4C2 4C3 0.000 0.0 180.0 0.0 0.000 ! PAMAM patch to connect to N2 as follows ! residue 1 is the N2 tail ! residue 2 is the C1 head one ! resiude 3 is the C1 head two ! 2C1---- ! / ! ---1N2 ! \ ! 3C1---- PRES DEND DELE ATOM 1H10 DELE ATOM 1H11 DELE ATOM 2H12 DELE ATOM 3H12 GROUP ATOM 1N2 NT -0.10 ATOM 2C1 CT -0.05 ATOM 2H1 HA 0.05 ATOM 2H2 HA 0.05 ATOM 3C1 CT -0.05 ATOM 3H1 HA 0.05 ATOM 3H2 HA 0.05 BOND 1N2 2C1 BOND 1N2 3C1 THET 1C5 1N2 2C1 THET 1N2 2C1 2C2 THET 1N2 2C1 2H1 THET 1N2 2C1 2H2 THET 1C5 1N2 3C1 THET 1N2 3C1 3C2 THET 1N2 3C1 3H1 THET 1N2 3C1 3H2 THET 2C1 1N2 3C1 DIHE 1C4 1C5 1N2 2C1 DIHE 1H8 1C5 1N2 2C1 DIHE 1H9 1C5 1N2 2C1 DIHE 1C4 1C5 1N2 3C1 DIHE 1H8 1C5 1N2 3C1 DIHE 1H9 1C5 1N2 3C1 DIHE 1C5 1N2 2C1 2C2 DIHE 1C5 1N2 2C1 2H1 DIHE 1C5 1N2 2C1 2H2 DIHE 1C5 1N2 3C1 3C2 DIHE 1C5 1N2 3C1 3H1 DIHE 1C5 1N2 3C1 3H2 DIHE 1N2 2C1 2C2 2C3 DIHE 1N2 2C1 2C2 2H3 DIHE 1N2 2C1 2C2 2H4 DIHE 1N2 3C1 3C2 3C3 DIHE 1N2 3C1 3C2 3H3 DIHE 1N2 3C1 3C2 3H4 DIHE 2C2 2C1 1N2 3C1 DIHE 2H1 2C1 1N2 3C1 DIHE 2H2 2C1 1N2 3C1 DIHE 2C1 1N2 3C1 3C2 DIHE 2C1 1N2 3C1 3H1 DIHE 2C1 1N2 3C1 3H2 ! my impropers IMPH 2H1 2C2 2C1 1N2 IMPH 3H1 3C2 3C1 1N2 IMPH 2C1 1C5 1N2 3C1 IMPH 2H1 1N2 2C1 2H2 IMPH 2H1 1N2 2C1 2C2 IMPH 3H1 1N2 3C1 3H2 IMPH 3H1 1N2 3C1 3C2 ! ! 2C2 dihedral is 90 rather than 180 to allow for tilt into ! H-bonding position upon minimization/dynamics IC 1C4 1C5 1N2 2C1 0.000 0.0 120.0 0.0 0.000 IC 1C4 1C5 1N2 3C1 0.000 0.0 -120.0 0.0 0.000 IC 1C5 1N2 2C1 2C2 0.000 0.0 090.0 0.0 0.000 IC 1N2 2C1 2C2 2C3 0.000 0.0 180.0 0.0 0.000 IC 1C5 1N2 3C1 3C2 0.000 0.0 180.0 0.0 0.000 IC 1N2 3C1 3C2 3C3 0.000 0.0 180.0 0.0 0.000 END ******** End of rtf *********** **************************************** Gus Mercier, Jr NIH - LDRR gmercier@helix.nih.gov **************************************** **************************************** Every attempt to employ mathematical methods in the study of chemical questions must be considered profoundly irrational and contrary to the spirit of chemistry ... If mathematical analysis should ever hold a prominent place in chemistry -- an aberration which is happily almost impossible -- it would occasion a rapid and widespread degeneration of that science. Auguste Comte Philosophie Positive, Paris, 1838 ------------------------------------------------------------- The underlying physical laws necessary for the mathematical theory of a large part of physics and the whole of chemistry are thus completely known, and the difficulty is only that the exact application of these laws leads to equations much too complicated to be soluble. Dirac, Proc. Roy. Soc (London) 123:714 (1929) ------------------------------------------------------------- From SUTJIANTO@cmt.anl.gov Mon May 20 18:54:14 1996 Received: from axp.cmt.anl.gov for SUTJIANTO@cmt.anl.gov by www.ccl.net (8.7.1/950822.1) id SAA23885; Mon, 20 May 1996 18:12:08 -0400 (EDT) Date: Mon, 20 May 1996 17:12:04 -0500 (CDT) From: Amin Sutjianto To: CHEMISTRY@www.ccl.net Message-Id: <960520171204.20c0011e@cmt.anl.gov> Subject: Cu basis set Hello everybody, I am looking for Cu basis set that can represent metal surface for CRYSTAL92. Thanks in advance. Amin From chpajt@bath.ac.uk Mon May 20 18:58:33 1996 Received: from goggins.bath.ac.uk for chpajt@bath.ac.uk by www.ccl.net (8.7.1/950822.1) id SAA23982; Mon, 20 May 1996 18:32:29 -0400 (EDT) Received: from bath.ac.uk (actually host mary.bath.ac.uk) by goggins.bath.ac.uk with SMTP (PP); Mon, 20 May 1996 23:32:19 +0100 Date: Mon, 20 May 1996 23:32:15 +0100 (BST) From: A J Turner To: "David E. Bernholdt" cc: Victor Anisimov , chemistry@www.ccl.net Subject: Re: CCL:M:MOPAC-93 memory requirements In-Reply-To: <199605201757.NAA10981@oldnova.npac.syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi! I don't know about mopac, but Charmm can do a similar thing. I think the problem is that if the largest single array gets bigger than your physical memory, the oppperating system cannot 'break it up'. This is probably a FORTRAN thing, as the arrays are contiguously assigned, rather than using pointers to point into blocks a dynamically allocated memory, as a C program _probably_ would do (well that's how I'd do it!). Cheers Alex +--------------------------------------------------+ |Alternate E-mail A.J.Turner@Bath.ac.uk | |www home @ http://www.bath.ac.uk/~chpajt/home.html| +--------------------------------------------------+