From chemistry-request@ccl.net Wed Jul 30 12:47:12 2003 Received: from aquarius.ime.eb.br (aquarius.ime.eb.br [200.20.120.44]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UGlB47008616 for ; Wed, 30 Jul 2003 12:47:12 -0400 Received: from epq.ime.eb.br (epq.ime.eb.br [200.20.120.217]) by aquarius.ime.eb.br (8.12.8/8.12.8) with ESMTP id h6UGl9I5006613 for ; Wed, 30 Jul 2003 13:47:10 -0300 Received: from EPQ/SpoolDir by epq.ime.eb.br (Mercury 1.48); 30 Jul 03 13:50:21 -0300 Received: from SpoolDir by EPQ (Mercury 1.48); 30 Jul 03 13:50:14 -0300 Received: from HELIO (200.20.123.196) by epq.ime.eb.br (Mercury 1.48) with ESMTP; 30 Jul 03 13:50:05 -0300 From: "Teodorico Ramalho" To: Subject: Transition Metal Parameters Date: Wed, 30 Jul 2003 13:46:51 -0300 Message-ID: <000001c356ba$2f98e180$c47b14c8@HELIO> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C356A1.0A4D3020" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C356A1.0A4D3020 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: 7bit Dear CCLs, I would like, if possible, of the vdw parameters of Zinc (Zn2+) and Cadmium (Cd2+) or some reference about this subject. I have found Zn parameters in MMFF94 and MM2 force fields, but I did not found cd parameters. Could anyone give me some information? Thanks a lot, Teodorico --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.502 / Virus Database: 300 - Release Date: 18/07/2003 --- Outgoing mail is certified Virus Free. Checked by AVG anti-virus system (http://www.grisoft.com). Version: 6.0.504 / Virus Database: 302 - Release Date: 24/07/2003 ------=_NextPart_000_0001_01C356A1.0A4D3020 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Dear CCLs,

 

I would like, if possible, of the vdw parameters of Zinc (Zn2+) = and Cadmium (Cd2+) or some reference about this subject.  I have found Zn parameters in = MMFF94 and MM2 force fields, but I did not found cd parameters. Could anyone give me some information?

 

Thanks a = lot,

 

Teodorico =

 


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------=_NextPart_000_0001_01C356A1.0A4D3020-- From chemistry-request@ccl.net Thu Jul 31 03:56:30 2003 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6V7uT47027485 for ; Thu, 31 Jul 2003 03:56:30 -0400 Received: from [136.206.1.18] by hawk.dcu.ie with HTTP; Thu, 31 Jul 2003 08:56:25 +0100 Date: Thu, 31 Jul 2003 08:56:25 +0100 Message-ID: <3EFBE2180001D1AA:at:hawk.dcu.ie> In-Reply-To: <001501c350c9$be985a10$52c453c8@xenon> From: noel.oboyle2:at:mail.dcu.ie Subject: RE: CCL:Atomic Orb. Coefficients in a Molecular Orbital analysis To: "Diego Venegas-Yazigi" Cc: Chemistry:at:CCL.net MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h6V7uU47027486 Check out sections 10 and 11 of the following course notes by Prof. Hendrik Zipse at the Ludwig-Maximilian-Universitdt : http://www.cup.uni-muenchen.de/oc/zipse/lv18099/topics.html. Essentially, the square of the coefficients is only equal to 1 if there isn't any overlap between different basis functions, e.g. NDO (neglect of differential overlap) schemes like several semi-empirical methods (INDO for example). In every other case, it is necessary to take into account the overlap integrals (you can get Gaussian to output these also by including IOP(3/33=1) in your route section). If you have any problems, send me an email. Noel O'Boyle >-- Original Message -- >From: "Diego Venegas-Yazigi" >To: "Computational Chemistry List" >Subject: CCL:Atomic Orb. Coefficients in a Molecular Orbital analysis >Date: Tue, 22 Jul 2003 23:22:53 -0400 > > >Dear CCLers > I am interested in a Molecular Orbital composition analysis. I did >Single Point calculations in Jaguar 4.2 and Gaussian 98 for Linux Rev A.9 >and in both calculations the sum of the squared coefficients (atomic orbital >coefficients) is not equal to 1, it is a different value for each MO. My >question is how to normalise each MO to get a total sum (of the squared AO >coefficients) equal to 1 (one). >Thanks a lot to all > >Diego Venegas-Yazigi > > >_________________________________________________ > Dr. Diego Venegas Yazigi >Postdoctoral Researcher >New Magnetic Materials Laboratory >Centre for the Advanced and Interdisciplinary >Research in Material Science (CIMAT) >Olivos 1007, Of. 313, Independencia, 8380492 >Santiago, CHILE >----- >W Ph. : 56 (2) 678-2801 >Mobile : 56 (9) 841-8497 >_________________________________________________ > > > > > > > > >---------------------------------------------------------------------------- >---- > > > > > > >-= This is automatically added to each message by mailing script =- >To send e-mail to subscribers of CCL put the string CCL: on your Subject: >line >and send your message to: CHEMISTRY:at:ccl.net > >Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net > >HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > >If your mail is bouncing from CCL.NET domain send it to the maintainer: >Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) >-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Wed Jul 30 15:10:09 2003 Received: from osgood.unet.maine.edu (osgood.unet.maine.edu [130.111.39.64]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UJA947011995 for ; Wed, 30 Jul 2003 15:10:09 -0400 Received: from adamantane.maine.edu (Adamantane.umecit.maine.edu [130.111.234.157]) by osgood.unet.maine.edu (8.11.6/8.11.6) with ESMTP id h6UJ9pX08442 for ; Wed, 30 Jul 2003 15:09:51 -0400 Message-Id: <5.1.1.6.0.20030730151419.00a162e0/at/mail.maine.edu> X-Sender: rcfort/at/mail.maine.edu (Unverified) X-Mailer: QUALCOMM Windows Eudora Version 5.1.1 Date: Wed, 30 Jul 2003 15:18:46 -0400 To: chemistry/at/ccl.net From: "Raymond C. Fort Jr." Subject: Compiling Molscript Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed X-MailScanner-Information: Please contact the ISP for more information X-MailScanner: Found to be clean Apologies if this is a bit off topic: I have been trying to compile Molscript under Linux (red Hat 6.2 or 7.2). I have fought through most of the problems with location and names of libraries (with the help of makefiles from Pierre Cotney and Edward Berry), but now I get the following error messages: -L/usr/X11R6/lib -lglut -lGLU -lGL -lXmu -lXext -lX11 -ljpeg -lpng -lgd -lz -lm opengl.o: In function `pick': opengl.o(.text+0x696): undefined reference to `ogl_check_errors' opengl.o: In function `ogl_render_init': opengl.o(.text+0x15b4): undefined reference to `ogl_check_errors' opengl.o: In function `ogl_render_lists': opengl.o(.text+0x1871): undefined reference to `ogl_check_errors' opengl.o: In function `ogl_cylinder': opengl.o(.text+0x2c7a): undefined reference to `ogl_cylinder_faces' opengl.o: In function `ogl_label': opengl.o(.text+0x31f7): undefined reference to `ogl_bitmap_string' opengl.o: In function `ogl_stick': opengl.o(.text+0x3916): undefined reference to `ogl_cylinder_faces' opengl.o: In function `ogl_render_lights': opengl.o(.text+0x6e6d): undefined reference to `ogl_check_errors' opengl.o: In function `ogl_sphere': opengl.o(.text+0x70f1): undefined reference to `ogl_sphere_faces_globe' collect2: ld returned 1 exit status make: *** [molscript] Error 1 Has anyone successfully completed this task who would be willing to share a makefile? Again, apologies to those who might consider this off topic, and thanks in advance for any help! Ray Professor Ray Fort Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine EMail: rcfort/at/maine.edu Orono, ME 04469 Web: chemistry.umeche.maine.edu/fort.html Molecular modeling of organic and biological molecules; wood and pulping chemistry From chemistry-request@ccl.net Wed Jul 30 19:50:58 2003 Received: from upstate.edu (gw4.upstate.edu [139.127.9.87]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UNow47017919 for ; Wed, 30 Jul 2003 19:50:58 -0400 Received: from HSCHOSP-MTA by upstate.edu with Novell_GroupWise; Wed, 30 Jul 2003 19:50:43 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 6.0.4 Beta Date: Wed, 30 Jul 2003 19:50:18 -0400 From: "Michael Chen" To: Subject: EWALD PME problem Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi, everyone, Hope all is well. Sorry to post here again for some pain in the neck. Everytime, when I used the command line in a multiple- processor run like this: NBONDED - EWALD PMEwald KAPPa 0.55 FFTX 81 FFTY 81 FFTZ 81 - ORDe 6 cutnb 10 ctofnb 8 ctonnb 7 cutim 10 - inbfrq -1 imgfrq -1 vdw vshift wmin 1.0 CHARMM just stopped right here, which never happened in a singular-processor run. Thus, in parallel mode, I had no way in using PME method, but using the commnad like: energy group switch cdiel - vgroup vswitch - ctonnb 8.0 ctofnb 11.0 cutnb 12.0 cutim 12.0 The machine I ran CHARMM on was SUN Solaris system with 30 processors. Could this be the hardware thing? Thank you very much for the answer and the time. May you have a nice day. ***************************************************** Michael Chen Department of Biochemistry & Pharmacology SUNY Upstate Medical University 750 East Adams Street Syracuse, NY 13210 USA ***************************************************** From chemistry-request@ccl.net Wed Jul 30 12:52:09 2003 Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UGq847008734 for ; Wed, 30 Jul 2003 12:52:08 -0400 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7+Sun/8.11.7/NAS-6n) with ESMTP id h6UGpnD24789; Wed, 30 Jul 2003 09:51:49 -0700 (PDT) Date: Wed, 30 Jul 2003 09:51:49 -0700 (PDT) From: Ioana Cozmuta To: Vlad Cojocaru cc: VMD , CCL , namd:at:ks.uiuc.edu Subject: Re: CCL:NAMD failure on Berendsen pressure scheme In-Reply-To: <3F27BFD3.9010709:at:mpi-bpc.mpg.de> Message-ID: References: <3F27BFD3.9010709:at:mpi-bpc.mpg.de> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Vlad, 1. You say that you did an NVT equilibration previous to the NPT dynamics you want to run. But there is nowhere in your script a command where you load the velocities from the file generated during equilibration (velocities file.vel). Why do you heat up your system if you do not use in the end the velocities of the solvent? I do not understand why you are going back to Temperature 100. 2. I usually also read the unit cell information from the xsc file from the previous equilibration extendedSystem file.xsc 3. You should be able to use a timestep of 2fs. I am not sure what water model you are using but with Shake/Rattle on this should work (it works for me). 4. Here is what I use for the Berendsen pressure coupling: berendsenPressure on berendsenPressureTarget 1.01325 berendsenPressureCompressibility 4.9e-5 berendsenPressureRelaxationTime 500 berendsenPressureFreq 1 5. I also define the other parameters (even if they are =1) fullElectFrequency 1 nonbondedFreq 1 stepspercycle 1 6. As a general rule, if something is not working, maybe you should look back at your heating procedure and minimization, plot out some parameters (T, Epotential, Etotal, Evdw..etc). Read Berendsen's paper about the way the temperature and pressure coupling works. 7. Read careful the information listed in the header of the NAMD output file (INFO), NAMD is sensitive to the name of the variables you define in your input file. And may read them wrong or not at all.If they are critical your simulation will not start at all but it may be that they are not critical for the simulation to run and still their value will be the default one Hope this helps, Ioana On Wed, 30 Jul 2003, Vlad Cojocaru wrote: > Dear fellows, > If you have some experience with namd could somebody explain why this > is happening (see error message at the bottom of the message)? I am > using the following script:. It is a constant pressure equilibration > using Berendsen algorithm for temp and pressure. This equilibration step > follows after a minim and a const Vol. eq in which the temperature is > adjusted to 300 (also with temp coupling scheme). The protocol below > works fine in AMBER but maybe there some differences between the values > used by the 2 programs that I didnt figure out. The first eq. at const > Vol works fine both in Amber and Namd so I guess there is something > about pressure here. If you want more details please let me know!. > I would appreciate any advice. Thank you very much , > Vlad > > # *** AMBER force field *** --------------------------------- > amber on > parmfile rnaWI.top > coordinates rnaWI_mdeq2.pdb.coor > readexclusions yes > exclude scaled1-4 > 1-4scaling 0.83333333 #=1/1.2 > scnb 2 > > #*** approximations for nonbonded interactions ------------ > switching off > cutoff 9 > stepspercycle 1 > > #***equilibration parameters > minimization off > numsteps 10000 > timestep 1.0 > > #***SHAKE use > rigidbonds all > > #***temperature regulation for equilibration step (NPT) using > #***temperature coupling > temperature 100.0 > tcouple on > tcoupletemp 300.0 > tcouplefile rnaWI_ceq2.pdb ### friction coef.=1.0 > tcouplecol B > > > #***constant pressure equilibration using Berendsen bath coupling > usegrouppressure on > useflexiblecell on > berendsenpressure on > berendsenpressuretarget 1.0 > berendsenpressurecompressibility 0.0000446 > berendsenpressurerelaxationtime 500 > berendsenpressurefreq 100 > > #***PME > PME on > cellBasisVector1 56.21 0 0 > cellBasisVector2 0 58.53 0 > cellBasisVector3 0 0 57.89 > cellOrigin 0 0 0 > PMEGridSizeX 50 > PMEGridSizeY 55 > PMEGridSizeZ 50 > XSTfile rnaWI_mdeq3.XST > XSTfreq 200 > > #***constraints (holding the solute fixed) > constraints on > consexp 2 > consref rnaWI_mdeq2.pdb.coor > conskfile rnaWI_res500.pdb > conskcol B > > #***outputnames > outputname rnaWI_mdeq3.pdb > restartname rnaWI_mdeq3.rst > dcdfile rnaWI_mdeq3.dcd > dcdfreq 200 > veldcdfile rnaWI_mdeq3.vel.dcd > veldcdfreq 200 > restartfreq 200 > outputenergies 100 > outputpressure 100 > binaryoutput off > binaryrestart off > > > > ###---error----------------- > > RESSURE: 300 76798.7 -40631.2 58693.1 -13378.6 29200.3 -5152.76 69223.5 > -42523.7 81493.1 > GPRESSURE: 300 76687.2 -40836.2 58854.3 -13914.7 29538.5 -4262.26 > 68552.2 -42832.5 81484.6 > ENERGY: 300 2002.7469 2400.4670 550.4454 0.0000 > -61779.2755 9089.4231 60866.5902 0.0000 31247.2457 44377.6430 > 1056.1747 62497.3627 62570.0965 185386.7344 -1757.5130 -1600.7691 > ERROR: Constraint failure in RATTLE algorithm for atom 121! > ERROR: Constraint failure; simulation has become unstable. > ERROR: Exiting prematurely. > ========================================== > > -- > Vlad Cojocaru > Max Planck Institute for Biophysical Chemistry > Department: 060 > Am Fassberg 11, 37077 Goettingen, Germany > tel: ++49-551-201.1327 > e-mail: Vlad.Cojocaru:at:mpi-bpc.mpg.de > home tel: ++49-551-9963204 > > > > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY:at:ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST:at:ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl:at:ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Wed Jul 30 11:13:53 2003 Received: from mail-a.bcc.ac.uk (mail-a.bcc.ac.uk [144.82.100.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h6UFDq47006210 for ; Wed, 30 Jul 2003 11:13:53 -0400 Received: from pop-b.ucl.ac.uk by mail-a.bcc.ac.uk with SMTP (Mailer) with ESMTP; Wed, 30 Jul 2003 16:13:44 +0100 Received: from socrates-a.ucl.ac.uk (socrates-a.ucl.ac.uk [144.82.100.160]) by pop-b.ucl.ac.uk (8.11.7+Sun/8.9.3) with ESMTP id h6UFDdi28993; Wed, 30 Jul 2003 16:13:39 +0100 (BST) Date: Wed, 30 Jul 2003 16:13:39 +0100 (BST) From: Graeme Day To: Peter Oledzki cc: chemistry Subject: Re: CCL:Standard Bond Lengths? In-Reply-To: <03073012130100.31948@bmbpcu21> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-UCL-MailScanner: Found to be clean There might be something more recent, but this is a useful tabulation of observed (crystal structure) average bond lengths: "Tables of Bond Lengths determined by X-Ray and Neutron Diffraction. Part 1. Bond Lengths in Organic Compounds" J.Chem.Soc. Perkin Trans.2 (1987) S1-S19. Hope that helps, Graeme --- Graeme M. Day Centre for Theoretical and Computational Chemistry Department of Chemistry tel (0)20 7679 4665 University College London fax (0)20 7679 7463 20 Gordon St., London email: g.day!at!ucl.ac.uk WC1H 0AJ, UK On Wed, 30 Jul 2003, Peter Oledzki wrote: > Hello CCLers, > > I'm looking for standard bond lengths between various atoms in organic > molecules. I'm using these bond lengths in a molecular mechanics force field > (GRID) for flexible ligand docking. I require bond lengths between each atom > type i.e. an aromatic carbon and an sp3 NH group with a lone pair etc etc > > Does anybody know of any resources avialable ? Like a database or websites? > > Any help on this matter would be greatly appreciated > > Cheers > > Peter > > -- > *********************************************************** > Peter Oledzki > PhD Bioinformatics Research Student > School of Biochemistry and Molecular Biology > University of Leeds > LS2 9JT > 0113 3432988 > > > -= This is automatically added to each message by mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY!at!ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST!at!ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl!at!ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > >