From owner-chemistry@ccl.net Tue Jul 18 00:25:01 2006 From: "Renata Anna Kwiecien renee+*+p.lodz.pl" To: CCL Subject: CCL: TS for Me(II) complex Message-Id: <-32171-060718002236-5926-akW1JZ8e2cyKTaQm3Aeieg,,server.ccl.net> X-Original-From: "Renata Anna Kwiecien" Date: Tue, 18 Jul 2006 00:22:35 -0400 Sent to CCL by: "Renata Anna Kwiecien" [renee*o*p.lodz.pl] Dear all, Can anyone give me some hints or point out papers on locating transition state for cis-trans isomerization in complexes of Metal(II) coordinated by oxygen and nitrogen atoms with two identical ligands - naphthalene analogs? Cis and trans isomers are square-planar complexes. Thank you, Renata ***************************************** Renata Anna Kwiecien Institute of Applied Radiation Chemistry Technical University of Lodz ul. Zeromskiego 116 90-924 Lodz, Poland e-mail: renee=p.lodz.pl ***************************************** From owner-chemistry@ccl.net Tue Jul 18 05:46:00 2006 From: "Roger Robinson r.robinson:imperial.ac.uk" To: CCL Subject: CCL:G: Gaussian Default.Route File Message-Id: <-32172-060718054512-20890-JZAKDZ8elNIlZKjjCP0zdQ%server.ccl.net> X-Original-From: "Roger Robinson" Date: Tue, 18 Jul 2006 05:45:10 -0400 Sent to CCL by: "Roger Robinson" [r.robinson%imperial.ac.uk] Hi, When running gaussian I seem to be using ever larger amount of scratch space. I've tried to limit this using the Default.Route file. I creating this is g03root/g03. and added the line -- MaxDisk=40GB as specified in the Gaussian manual. http://www.gaussian.com/g_ur/m_defroute.htm However Gaussian seems to be ignoring it. Have I put it in the right place ? Thanks Roger From owner-chemistry@ccl.net Tue Jul 18 06:20:00 2006 From: "Jens Spanget-Larsen spanget]~[ruc.dk" To: CCL Subject: CCL:G: Normal mode displacement in GAUSSIAN Message-Id: <-32173-060718061823-9463-XQgbHFkI4CAcusvWbDmiOg~~server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Jul 2006 12:18:06 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget],[ruc.dk] Karl and Hiro, the cartesian displacement vector X (dimension = distance) associated with the normal coordinate Q (dimension = distance * mass^(1/2)) is given by X = mu^(-1/2) * Q, where mu is the reduced mass [1]. The X vectors for different normal modes have different lengths; e.g., heavy nuclei tend to move shorter distances than light nuclei. However, the "normal coordinates" (d) printed by GAUSSIAN are the cartesian displacement vectors normalized to unit distance. To derive the vector X > from the the GAUSSIAN output you simply multiply the printed coefficients (d) by the inverse square root of the pertinent reduced mass, mu^(-1/2). Jens >--< [1] Reduced mass: Let a normal coordinate be given by Q = SUM{i}[c(i) * q(i)], q(i) = m(i)^(1/2) * x(i) where the sum is over the 3N mass-weighted nuclear displacement coordinates q(i), m(i) are the corresponding nuclear masses, and x(i) the cartesian displacement coordinates. If Q is normalized to unity, the reduced mass mu is given by mu = 1 / SUM{i}[c(i)^2 / m(i)] The reduced mass mu is related to the harmonic angular frequency w and harmonic force constant k through w^2 = k/mu. ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget,,ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Karl Irikura karl.irikura-#-nist.gov wrote: > Sent to CCL by: Karl Irikura [karl.irikura .. nist.gov] > > > Hi. I believe the NMs in Gaussian are in units of distance (without > mass weighting) and are normalized to 1 unit of distance. If that's > correct, you need to add the mass weights and then renormalize to get > "standard" NM vectors. I've forgotten what the red. mass is, but > it's probably just the normalization factor. > > Good luck, > > Karl > > At 12:32 AM 7/13/2006, you wrote: > >>Sent to CCL by: "Hiro Maekawa" [hmaekawa!A!uci.edu] >>Dear CCL, >> >>I have difficulty in understanding normal mode displacement obtained > >>from GAUSSIAN03 package. I have read a paper in the GAUSSIAN website > >>("vibrational analysis in GAUSSIAN") and checked the CCL archive, >>but it is still not clear whether I am correct or not. >> >>I would like to get a matrix L which relates normal mode coordinate >>Q [angstrom*(amu)1/2] and cartesian coordinate x [angstrom] of 3N >>atoms, that is x=LQ. >> >>In the GAUSSIAN output file, you can get normal coordinate which >>does not have any unit as follows. >> >> incident light, reduced masses (AMU), force constants (mDyne/A), >> and normal coordinates: >> Atom >>AN X Y Z X Y Z X Y Z >> 1 6 0.00 0.00 0.00 0.00 0.00 0.03 0.00 >>0.00 0.07 >> 2 8 0.00 0.00 0.04 0.00 0.00 0.06 0.00 >>0.00 0.03 >> 3 7 0.00 0.00 -0.06 0.00 0.00 0.00 0.00 >>0.00 0.30 >> >>My concerns are... >>1. These displacements are normalized by multiplying by square root >>of the reduced mass, and hence are dimensionless. I need to divide >>by it to obtain the original numbers. >> >>2. The numbers I get after the process 1 are elements of the >>trasposed matrix of L (=tL), that is Q=(tL)x. >> >>If these are wrong, please tell me the correct. >>I appreciate your help. From owner-chemistry@ccl.net Tue Jul 18 07:42:00 2006 From: "Laxmikanth Rao Joshi lkjoshiji|,|yahoo.com" To: CCL Subject: CCL: Input for Nanohub; lkjoshiji-*-yahoo.com Message-Id: <-32174-060718060024-31317-EGRTAdgDF4nfe7jSTPhgpQ-*-server.ccl.net> X-Original-From: "Laxmikanth Rao Joshi" Date: Tue, 18 Jul 2006 06:00:23 -0400 Sent to CCL by: "Laxmikanth Rao Joshi" [lkjoshiji|*|yahoo.com] Hi to all I am trying to do some calculation for dna base pair using NANOHUB. I have given the input in the same fashion as the authors of nanohub were described. I am getting positive HOMO and LUMO values. Hope I am going somewhere wrong in giving the input. Please suggest me how to give the input for dna base pair. Thanks in advance Cheers Laxmikanth Rao Joshi From owner-chemistry@ccl.net Tue Jul 18 10:13:00 2006 From: "Gerard Pujadas gerard.pujadas- -urv.cat" To: CCL Subject: CCL: Residues involved in hydrophobic contact with ligands in PDB files Message-Id: <-32175-060718101102-17727-jfV6tO3fFToEnzxvQTowRw(!)server.ccl.net> X-Original-From: "Gerard Pujadas" Date: Tue, 18 Jul 2006 10:11:02 -0400 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas_-_urv.cat] Dear CCL list members, I wonder if there is a program, apart from LigPlot, that takes a PDB file of a protein-ligand complex and lists which are the residues involved in hydrophobic contacts or interactions with the ligand. With many thanks in advances for your help Yours sincerely Gerard From owner-chemistry@ccl.net Tue Jul 18 10:47:01 2006 From: "Gerard Pujadas gerard.pujadas- -urv.cat" To: CCL Subject: CCL: Calculation of protein's active site surface buried by a ligand Message-Id: <-32176-060718101350-18253-9pM+WR8BOeLJOLKh6eneBw::server.ccl.net> X-Original-From: "Gerard Pujadas" Date: Tue, 18 Jul 2006 10:13:50 -0400 Sent to CCL by: "Gerard Pujadas" [gerard.pujadas**urv.cat] Dear CCL list members, I wonder if there is a program that takes a PDB file of a protein-ligand complex and calculates the area of the protein's active site surface that it is buried by the contact with all or part of the ligand. With many thanks in advances for your help Yours sincerely Gerard From owner-chemistry@ccl.net Tue Jul 18 11:22:01 2006 From: "Olalla Nieto Faza faza++uvigo.es" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32177-060717152114-12496-em5pTxP4vAx7vF19ejgd+A---server.ccl.net> X-Original-From: Olalla Nieto Faza Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Jul 2006 13:20:58 -0500 MIME-Version: 1.0 Sent to CCL by: Olalla Nieto Faza [faza###uvigo.es] I've found these two to be good textbooks and useful for someone without any background on the field. However, depending on the kind of work you are doing, there are also other texts more focused in applications and less in algorithms that might suit you better. ]^[Book{Frenkel_Book_MolecularSimulation_2002, author = {Frenkel, Daan and Smit, Berend}, title = {{Understanding Molecular Simulation}}, publisher = {Academic Press}, year = 2002, edition = 2, } ]^[Book{Allen_Book_Computer_Simulation_Liquids_1987, author = {M.P. {Allen} and D.J. {Tildesley}}, title = {{Computer Simulation of Liquids}}, publisher = {Oxford University Press}, year = 1987, } I hope it helps. Olalla andras.borosy]-[givaudan.com wrote: > Sent to CCL by: andras.borosy ~~ givaudan.com > This is a multipart message in MIME format. > --=_alternative 004BF3AAC12571AE_= > Content-Type: text/plain; charset="ISO-8859-2" > Content-Transfer-Encoding: quoted-printable > > Dear Colleagues, > > Might anyone suggest me a good text book on molecular dynamics? > > Many thank in advance, > > -- --------------------------------------------------------------------- Olalla Nieto Faza 101 Smith Hall Ph:(612) 625-6317 Univ. of Minnesota faza]^[chem.umn.edu 207 Pleasant Street SE http://theory.chem.umn.edu/~faza/ Minneapolis, MN 55455-0431 (USA) --------------------------------------------------------------------- From owner-chemistry@ccl.net Tue Jul 18 11:57:01 2006 From: "Wayne Steinmetz WES04747*pomona.edu" To: CCL Subject: CCL: Solvation of organic molecules (with GROMACS) Message-Id: <-32178-060717220925-5344-h7v+U/Z01R6x9TQ7FULQkQ{=}server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 17 Jul 2006 18:30:58 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747_._pomona.edu] I use SYBYL for tasks such as these. SYBYL was originally written to handle small organic molecules but now has modules for macromolecules. Wayne E. Steinmetz Carnegie Professor of Chemistry Woodbadge Course Director Chemistry Department Pomona College 645 North College Avenue Claremont, California 91711-6338 USA phone: 1-909-621-8447 FAX: 1-909-607-7726 Email: wsteinmetz(a)pomona.edu WWW: pages.pomona.edu/~wsteinmetz -----Original Message----- > From: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net] Sent: Monday, July 17, 2006 4:38 PM To: Wayne Steinmetz Subject: CCL: Solvation of organic molecules (with GROMACS) Sent to CCL by: "Fernando D. Vila" [fer ~~ phys.washington.edu] Hello everyone.. A summer student and I are trying to simulate the solvation of some organic molecules. What we want is something that is very black-box: we give it a molecule, a solvent, we choose a force field, set up some MD parameters and we running. I'm sure there is a solution "out there", it looks like a pretty easy problem. We don't need anything very sophisticated since we are just trying to generate some MD snapshots to use in explicit solvent ab initio calculations of UV-Vis spectra (we just want to check a couple of ideas). He downloaded GROMACS and got it running. The problem he run into is that, although it is very easy to generate inputs for solvated ions and solvated polypeptides, it isn't very clear how to generate them for an arbitrary organic molecule like, say, benzene or aniline. I'm willing to drop GROMACS if anyone thinks there is an easier solution. Any suggestions will be quite welcome. Best regards, Fer. Ubi dubium ibi libertas. ************************************************************************ ******* Fernando D. Vila Voice (206)543-9697 Department of Physics Fax (206)685-0635 University of Washington E-mail fdv[A]u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv ************************************************************************ *******http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. From owner-chemistry@ccl.net Tue Jul 18 12:41:00 2006 From: "Maurizzio Argonni m.argonni() gmail.com" To: CCL Subject: CCL: Residues involved in hydrophobic contact with ligands in PDB files Message-Id: <-32179-060718123748-15152-QmloTUiUrI89ry2IK6ydiA]=[server.ccl.net> X-Original-From: "Maurizzio Argonni" Content-Type: multipart/alternative; boundary="----=_Part_27973_15518678.1153237399294" Date: Tue, 18 Jul 2006 11:43:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Maurizzio Argonni" [m.argonni^gmail.com] ------=_Part_27973_15518678.1153237399294 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hello Gerard, Check the LPC (Ligand-Protein Contact) server at http://bip.weizmann.ac.il/oca-bin/lpccsu Hope this helps. Maurizzio On 7/18/06, Gerard Pujadas gerard.pujadas- -urv.cat wrote: > > Sent to CCL by: "Gerard Pujadas" [gerard.pujadas_-_urv.cat] > Dear CCL list members, > > I wonder if there is a program, apart from LigPlot, that takes a PDB file > of a protein-ligand complex and lists which are the residues involved in > hydrophobic contacts or interactions with the ligand. > > With many thanks in advances for your help > > Yours sincerely > > Gerard> > > > ------=_Part_27973_15518678.1153237399294 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hello Gerard,
 
Check the LPC (Ligand-Protein Contact) server at http://bip.weizmann.ac.il/oca-bin/lpccsu
 
Hope this helps.
 
Maurizzio

 
On 7/18/06, Gerard Pujadas gerard.pujadas- -urv.cat <owner-chemistry#%#ccl.net> wrote:
Sent to CCL by: "Gerard  Pujadas" [gerard.pujadas_-_urv.cat]
Dear CCL list members,

I wonder if there is a program, apart from LigPlot, that takes a PDB file of a protein-ligand complex and lists which are the residues involved in hydrophobic contacts or interactions with the ligand.

With many thanks in advances for your help

Yours sincerely

Gerard



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------=_Part_27973_15518678.1153237399294-- From owner-chemistry@ccl.net Tue Jul 18 13:23:02 2006 From: "Alessandro Contini alessandro.contini{}unimi.it" To: CCL Subject: CCL: Solvation of organic molecules (with GROMACS) Message-Id: <-32180-060718132227-6413-Dnz12I81SPgCT0Ucq1T6JQ]^[server.ccl.net> X-Original-From: Alessandro Contini Content-transfer-encoding: 7BIT Content-type: text/plain Date: Tue, 18 Jul 2006 19:07:45 +0200 MIME-version: 1.0 Sent to CCL by: Alessandro Contini [alessandro.contini**unimi.it] Hi, you could try to use VMD/NAMD that are freely downloadable from http://www.ks.uiuc.edu/ (previous registration). Moreover they can be easily installed on all most common platforms. With NAMD it's quite easy getting started, thanks also to well done tutorials, and VMD it's a powerful graphic interface. In order to work with organic molecules the harder part is generating the topology file, however you could find another nice tutorial for this at http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf Anyway, it could be harder to simulate solvents different than water..."black boxes" as you mean do exist, but usually are commercial (and quite expensive) software. Hope this help Alessandro Il giorno lun, 17/07/2006 alle 20.55 -0400, Fernando D. Vila fer#% #phys.washington.edu ha scritto: > Sent to CCL by: "Fernando D. Vila" [fer ~~ phys.washington.edu] > Hello everyone.. > > A summer student and I are trying to simulate the solvation of some > organic molecules. What we want is something that is very black-box: we > give it a molecule, a solvent, we choose a force field, set up some MD > parameters and we running. I'm sure there is a solution "out there", it > looks like a pretty easy problem. We don't need anything very > sophisticated since we are just trying to generate some MD snapshots to > use in explicit solvent ab initio calculations of UV-Vis spectra (we just > want to check a couple of ideas). > > He downloaded GROMACS and got it running. The problem he run into is > that, although it is very easy to generate inputs for solvated ions and > solvated polypeptides, it isn't very clear how to generate them for an > arbitrary organic molecule like, say, benzene or aniline. > > I'm willing to drop GROMACS if anyone thinks there is an easier > solution. > > Any suggestions will be quite welcome. > > Best regards, Fer. > > Ubi dubium ibi libertas. > ******************************************************************************* > Fernando D. Vila Voice (206)543-9697 > Department of Physics Fax (206)685-0635 > University of Washington E-mail fdv[A]u.washington.edu > Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv > *******************************************************************************> > > -- Dr. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Universita' degli Studi di Milano, Facolta' di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini#%#unimi.it skype alessandrocontini From owner-chemistry@ccl.net Tue Jul 18 16:32:00 2006 From: "David van der Spoel spoel(0)xray.bmc.uu.se" To: CCL Subject: CCL: Solvation of organic molecules (with GROMACS) Message-Id: <-32181-060718162741-12324-eA8LMfjt548O/LFSy9iH9Q%%server.ccl.net> X-Original-From: David van der Spoel Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 18 Jul 2006 21:44:25 +0200 MIME-Version: 1.0 Sent to CCL by: David van der Spoel [spoel%x%xray.bmc.uu.se] Alessandro Contini alessandro.contini{}unimi.it wrote: > Sent to CCL by: Alessandro Contini [alessandro.contini**unimi.it] > Hi, you could try to use VMD/NAMD that are freely downloadable from > http://www.ks.uiuc.edu/ (previous registration). Moreover they can be > easily installed on all most common platforms. > With NAMD it's quite easy getting started, thanks also to well done > tutorials, and VMD it's a powerful graphic interface. In order to work > with organic molecules the harder part is generating the topology file, > however you could find another nice tutorial for this at > > http://www.ks.uiuc.edu/Training/Tutorials/science/topology/topology-tutorial.pdf > > Anyway, it could be harder to simulate solvents different than > water..."black boxes" as you mean do exist, but usually are commercial > (and quite expensive) software. > It is quite easy with gromacs too, for a molecule like benzene, and quite well described in the manual (chapter 5). For more complex molecules you can start with a topology from the prodrg server http://davapc1.bioch.dundee.ac.uk/programs/prodrg/prodrg.html which generates topologies for a number of programs and force fields, including gromacs. > Hope this help > > Alessandro > > > > > Il giorno lun, 17/07/2006 alle 20.55 -0400, Fernando D. Vila fer#% > #phys.washington.edu ha scritto: > >>Sent to CCL by: "Fernando D. Vila" [fer ~~ phys.washington.edu] >>Hello everyone.. >> >> A summer student and I are trying to simulate the solvation of some >>organic molecules. What we want is something that is very black-box: we >>give it a molecule, a solvent, we choose a force field, set up some MD >>parameters and we running. I'm sure there is a solution "out there", it >>looks like a pretty easy problem. We don't need anything very >>sophisticated since we are just trying to generate some MD snapshots to >>use in explicit solvent ab initio calculations of UV-Vis spectra (we just >>want to check a couple of ideas). >> >> He downloaded GROMACS and got it running. The problem he run into is >>that, although it is very easy to generate inputs for solvated ions and >>solvated polypeptides, it isn't very clear how to generate them for an >>arbitrary organic molecule like, say, benzene or aniline. >> >> I'm willing to drop GROMACS if anyone thinks there is an easier >>solution. >> >> Any suggestions will be quite welcome. >> >>Best regards, Fer. >> >>Ubi dubium ibi libertas. >>******************************************************************************* >>Fernando D. Vila Voice (206)543-9697 >>Department of Physics Fax (206)685-0635 >>University of Washington E-mail fdv[A]u.washington.edu >>Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv >>*******************************************************************************> >> >> -- David. ________________________________________________________________________ David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel=-=xray.bmc.uu.se spoel=-=gromacs.org http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++