From owner-chemistry@ccl.net Wed May 24 06:43:00 2006 From: "Peter Burger chburger : aci.unizh.ch" To: CCL Subject: CCL: C2v pointgroup & coordinate system / unique choices of axis Message-Id: <-31821-060524064030-3865-nM9HDi7z4eLaYBu6Rd7UMw a server.ccl.net> X-Original-From: "Peter Burger" Date: Wed, 24 May 2006 06:40:26 -0400 Sent to CCL by: "Peter Burger" [chburger*aci.unizh.ch] Dear CCLers, the following has puzzled me for a while... In the C2v point group different choices have been made in the literature with regard to the x and y axis. Several books on symmetry and point groups provide different answers... and sometimes even choose use them either way in different chapters. For water for instance, most of them opt for the xz plane as the molecular plane with y pependicular to it while others refer to the yz as molecular plane with x perpendicular to it. This obviously leads to a change of the b1 and b2 symbols and makes comparisons somehow complicated... So I guess my question is - use Al Cottons or Tinkhams book as authorities? Is there somewhere the _real_ truth? Cheers Peter From owner-chemistry@ccl.net Wed May 24 08:48:00 2006 From: "Miro Moman miromoman%a%gmail.com" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31822-060524071006-18822-m/tnUWX/mB+LPLbghNs37g[A]server.ccl.net> X-Original-From: "Miro Moman" Date: Wed, 24 May 2006 07:10:04 -0400 Sent to CCL by: "Miro Moman" [miromoman : gmail.com] Hello, I am currently modelling protein/DNA complexes. In both protein and DNA structures there are missing atoms/residues. For proteins, I know a number of freely avaliable programs that "guess" the coordinates of the non-resolved atoms and try to reconstruct the structure accordingly (such as SPDBV). However, I could not find any free program able to "correct" the DNA structures in a similar way (the only one I know is LeAP, which comes with the AMBER package). I would very much appreciate any information on such a program. Miro From owner-chemistry@ccl.net Wed May 24 10:01:01 2006 From: "Lisa Batsch lbatsch^-^gmail.com" To: CCL Subject: CCL:G: Compiling Gaussian to C code Message-Id: <-31823-060524094130-21185-vT9UqPQ0dFwthJqJeFZvaw{:}server.ccl.net> X-Original-From: "Lisa Batsch" Date: Wed, 24 May 2006 09:41:28 -0400 Sent to CCL by: "Lisa Batsch" [lbatsch[]gmail.com] Greetings! I am trying to run Gaussian in a parallel platform simulator to look at performance optimizations, but the simulator libraries only work with C. I am attempting to use F2C to compile the code to C and then run it and evaluate the output. When I try to do this it fails looking for a file f2c-dum.c Does anyone have this file and/or iformation oabout what it is needed for? Thank you, Lisa Batsch University of Central Florida From owner-chemistry@ccl.net Wed May 24 10:35:01 2006 From: "Konrad Hinsen konrad.hinsen() cea.fr" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31824-060524094348-21940-peijPlaOKHMmUHtwjNbSiw---server.ccl.net> X-Original-From: "Konrad Hinsen" Date: Wed, 24 May 2006 09:43:44 -0400 Sent to CCL by: "Konrad Hinsen" [konrad.hinsen:cea.fr] On 24.05.2006, at 14:53, Miro Moman miromoman%a%gmail.com wrote: I am currently modelling protein/DNA complexes. In both protein and DNA structures there are missing atoms/residues. For proteins, I know a number of freely avaliable programs that "guess" the coordinates of the non-resolved atoms and try to reconstruct the structure accordingly (such as SPDBV). However, I could not find any free program able to "correct" the DNA structures in a similar way (the only one I know is LeAP, which comes with the AMBER package). I would very much appreciate any information on such a program. The Molecular Modelling Toolkit (MMTK), available from http://dirac.cnrs-orleans.fr/MMTK/ will do this for proteins, DNA, and most other organic molecules. *However*, it can compute missing coordinates only for hydrogen atoms. -- ------------------------------------------------------------------------------- Konrad Hinsen Laboratoire Leon Brillouin (CEA-CNRS), CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: konrad.hinsen---cea.fr ------------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed May 24 11:10:00 2006 From: "Dominic Ryan dominic.ryan[*]comcast.net" To: CCL Subject: CCL: DNA modelling (missing atoms in PDB files) Message-Id: <-31825-060524100424-28225-ALyIErVk+R1PnUcRnOFAgw[#]server.ccl.net> X-Original-From: "Dominic Ryan" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 May 2006 10:01:44 -0400 MIME-Version: 1.0 Sent to CCL by: "Dominic Ryan" [dominic.ryan/a\comcast.net] Hello Miro, This is essentially a small homology building problem, but I think it is important to treat is as such. Missing atoms imply missing density, usually. This is often because of flexibility. This in turn means that you may have multiple equivalent solutions for where the atoms should be and you will need to consider which single solution, or set of solutions, is appropriate based on other information about the structure. Depending on your need, a simple cut and paste and equilibration from another closely related structure might work, expecially in the DNA, less assuredly in the protein. One of the web servers for model building might be ok if the changes are not large. See swiss-model for eg. or look for other examples in google searches. For a more sophisticated treatment I suggest one of several homology modeling methods such as embodied in MOE or Modeller or others. For an academic these can be either free or lower cost. Dominic Ryan -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] Sent: Wednesday, May 24, 2006 7:54 AM To: Ryan, M Dominic Subject: CCL: DNA modelling (missing atoms in PDB files) Sent to CCL by: "Miro Moman" [miromoman : gmail.com] Hello, I am currently modelling protein/DNA complexes. In both protein and DNA structures there are missing atoms/residues. For proteins, I know a number of freely avaliable programs that "guess" the coordinates of the non-resolved atoms and try to reconstruct the structure accordingly (such as SPDBV). However, I could not find any free program able to "correct" the DNA structures in a similar way (the only one I know is LeAP, which comes with the AMBER package). I would very much appreciate any information on such a program. Mirohttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 24 12:01:00 2006 From: "Russell D Johnson III russell.johnson%a%nist.gov" To: CCL Subject: CCL: C2v pointgroup & coordinate system convention Message-Id: <-31826-060524115155-28582-/6eLz3RywTFuU7HfehwNIg .. server.ccl.net> X-Original-From: Russell D Johnson III Content-Type: text/plain; charset="us-ascii" Date: Wed, 24 May 2006 11:13:46 -0400 Mime-Version: 1.0 Sent to CCL by: Russell D Johnson III [russell.johnson++nist.gov] Hello, For planar C2v molecules the convention is to have the x-axis out of the plane. This and other similar recommendations were published in the Journal of Chemical Physics 23(11), page 1997, 1955 "Report on Notation for the Spectra of Polyatomic Molecules". Unfortunately there are a lot of spectroscopy papers published before this using one or the other direction for the x-axis, and not everyone since has chosen to follow this recommendation. It's also a good idea to explicitly state what coordinated system is being used. Russ Johnson At 07:10 2006-05-24, you wrote: >Sent to CCL by: "Peter Burger" [chburger*aci.unizh.ch] >Dear CCLers, > >the following has puzzled me for a while... > >In the C2v point group different choices have been made in the >literature with regard to the x and y axis. > >Several books on symmetry and point groups provide >different answers... and sometimes even choose use >them either way in different chapters. > >For water for instance, most of them opt for the xz plane >as the molecular plane with y pependicular to it while others >refer to the yz as molecular plane with x perpendicular to it. > >This obviously leads to a change of the b1 and b2 symbols >and makes comparisons somehow complicated... > >So I guess my question is - use Al Cottons or Tinkhams >book as authorities? Is there somewhere the _real_ truth? > >Cheers > >Peter Dr. Russell D. Johnson III Research Chemist National Institute of Standards and Technology Computational Chemistry Group 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301+975-2513 fax:301+869-4020 email: russell.johnson|a|nist.gov From owner-chemistry@ccl.net Wed May 24 12:35:00 2006 From: "Carsten Detering detering_._biosolveit.de" To: CCL Subject: CCL: 4th FlexX Workshop: Early Bird Dead Line Reminder - Location update Message-Id: <-31827-060524122145-14414-UNx87URgxW7cVfCZQnK2iA/./server.ccl.net> X-Original-From: "Carsten Detering" Date: Wed, 24 May 2006 12:21:44 -0400 Sent to CCL by: "Carsten Detering" [detering-,-biosolveit.de] Dear CClers, The early bird deadline for the 4th FlexX Docking Workshop is running out on Wednesday, May 31st, 2006 Hurry up and get your reduced rate for this premier event. The location for this year's workshop will be at the SUN campus, Santa Clara, CA. Please visit our web site for directions, and how to register for the workshop: http://www.biosolveit.de/workshops/2006 We are looking forward to seeing you in the Bay Area! -your developers of FlexX ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ LOCATION UPDATED! The 4th FlexX DOCKING WORKSHOP will take place September 7-8, 2006 at the SUN Campus, Santa Clara, California, USA back-to-back with the ACS Fall Meeting. http://www.biosolveit.de/workshops/2006 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-chemistry@ccl.net Wed May 24 15:37:01 2006 From: "Andrew D. Fant fant\a/pobox.com" To: CCL Subject: CCL:G: Compiling Gaussian to C code Message-Id: <-31828-060524151130-23403-/o8P1ibP953CLaG6M4rXRw * server.ccl.net> X-Original-From: "Andrew D. Fant" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 24 May 2006 14:12:37 -0400 MIME-Version: 1.0 Sent to CCL by: "Andrew D. Fant" [fant^^pobox.com] Lisa Batsch lbatsch^-^gmail.com wrote: > Sent to CCL by: "Lisa Batsch" [lbatsch[]gmail.com] > Greetings! > > I am trying to run Gaussian in a parallel platform simulator to look at performance optimizations, but the simulator libraries only work with C. > > I am attempting to use F2C to compile the code to C and then run it and evaluate the output. When I try to do this it fails looking for a file f2c-dum.c > > Does anyone have this file and/or iformation oabout what it is needed for? > Lisa, I don't know about the f2c-dum.c file, but I don't think you will get very far with using f2c as a substitute for a tool that actually understands Fortran. The c code that f2c generates is legal c, and will compile, but it's not exactly idiomatic, and the documentation, as I recall, discourages making changes to the code in its c form. It's something of a hack. that only really understands strict ansi f77, to compile dusty deck code on machines without Fortran compilers and not a full-scale migration tool. I'm not sure how well it would handle the memory overlays that Gaussian likes to use either. I don't mean to sound negative, but I wanted to warn you before you possibly throw a lot of time away fighting your toolset. HTH, Andy -- Andrew Fant | And when the night is cloudy | This space to let Molecular Geek | There is still a light |---------------------- fant[A]pobox.com | That shines on me | Disclaimer: I don't Boston, MA | Shine until tomorrow, Let it be | even speak for myself From owner-chemistry@ccl.net Wed May 24 18:47:00 2006 From: "Eric Hu list.eric%gmail.com" To: CCL Subject: CCL: freeze interval vibrations Message-Id: <-31829-060524173826-23608-99X3dMaXVpxz8BXrrsRS5g,,server.ccl.net> X-Original-From: "Eric Hu" Content-Type: multipart/alternative; boundary="----=_Part_24727_29052931.1148503596537" Date: Wed, 24 May 2006 13:46:36 -0700 MIME-Version: 1.0 Sent to CCL by: "Eric Hu" [list.eric_+_gmail.com] ------=_Part_24727_29052931.1148503596537 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, I am conducting an organic molecular assembly simulation (about 55 atom= s in each subunit and there are 12 subunit in total). I want to freeze the subunit internal vibration (saving sampling time) during md since I am more interested in the assembly process between subunits. Are there any suitable "rigid body" molecular dynamics packages for this purpose? Thank you. Eric ------=_Part_24727_29052931.1148503596537 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, I am conducting an organic molecular assembly simulation (about 55 atoms in each subunit and there are 12 subunit in total). I want to freeze the
subunit internal vibration (saving sampling time) during md since I am more interested in the assembly process between subunits.

Are there any suitable "rigid body" molecular dynamics packages f= or this purpose? Thank you.

Eric
------=_Part_24727_29052931.1148503596537-- From owner-chemistry@ccl.net Wed May 24 19:22:00 2006 From: "Nan Jiang nj12 ~ duke.edu" To: CCL Subject: CCL:G: How to calculate frequencydependent hyperpolarizability in Gaussian03? Message-Id: <-31830-060524180950-25875-6R59eHo5yTuc1cnzptpaTg(!)server.ccl.net> X-Original-From: "Nan Jiang" Date: Wed, 24 May 2006 18:09:48 -0400 Sent to CCL by: "Nan Jiang" [nj12#%#duke.edu] Dear all, I am using CPHF/3-21g POLAR=DCSHG in gaussian 03 to calculate the frequency-dependent hyperpolarizability. Finally I got 18 beta tensor elements. Does anyone know exactly what these 18 tensors are? Thanks very much! Best, Nan From owner-chemistry@ccl.net Wed May 24 20:38:00 2006 From: "zborowsk-*-chemia.uj.edu.pl" To: CCL Subject: CCL: C2v pointgroup & coordinate system / unique choices of axis Message-Id: <-31831-060524194412-13603-snU6ELEK669uhUAxnSVTrg,server.ccl.net> X-Original-From: zborowsk:-:chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Thu, 25 May 2006 01:00:05 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk- -chemia.uj.edu.pl > Sent to CCL by: "Peter Burger" [chburger*aci.unizh.ch] > Dear CCLers, > > the following has puzzled me for a while... > > In the C2v point group different choices have been made in the > literature with regard to the x and y axis. > > Several books on symmetry and point groups provide > different answers... and sometimes even choose use > them either way in different chapters. > > For water for instance, most of them opt for the xz plane > as the molecular plane with y pependicular to it while others > refer to the yz as molecular plane with x perpendicular to it. > > This obviously leads to a change of the b1 and b2 symbols > and makes comparisons somehow complicated... > > So I guess my question is - use Al Cottons or Tinkhams > book as authorities? Is there somewhere the _real_ truth? The truth is everywhere What is your problem connected with different orientation of water molecule. You can use both of them. They provide the same physical description > > Cheers > > Peter> > > > -- Krzysztof Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk,+,chemia.uj.edu.pl ICQ 158385743 gg 3817259 skype kzys70 From owner-chemistry@ccl.net Wed May 24 23:26:00 2006 From: "Gustavo Mercier gamercier||yahoo.com" To: CCL Subject: CCL: freeze interval vibrations Message-Id: <-31832-060524215148-22839-o5dLekg51a8hy2VhuJ3v4A---server.ccl.net> X-Original-From: Gustavo Mercier Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-411024957-1148518293=:34309" Date: Wed, 24 May 2006 17:51:33 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Gustavo Mercier [gamercier!A!yahoo.com] --0-411024957-1148518293=:34309 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi! You may try Moldy. It is rigid body molecular dynamics program that uses a quaternion implementation for rotations. A google search should get you the web site. Bye! GMercier "Eric Hu list.eric%gmail.com" wrote: Sent to CCL by: "Eric Hu" [list.eric_+_gmail.com] ------=_Part_24727_29052931.1148503596537 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, I am conducting an organic molecular assembly simulation (about 55 atom= s in each subunit and there are 12 subunit in total). I want to freeze the subunit internal vibration (saving sampling time) during md since I am more interested in the assembly process between subunits. Are there any suitable "rigid body" molecular dynamics packages for this purpose? Thank you. Eric ------=_Part_24727_29052931.1148503596537 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, I am conducting an organic molecular assembly simulation (about 55 atoms in each subunit and there are 12 subunit in total). I want to freeze the subunit internal vibration (saving sampling time) during md since I am more interested in the assembly process between subunits. Are there any suitable "rigid body" molecular dynamics packages f= or this purpose? Thank you. Eric ------=_Part_24727_29052931.1148503596537--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- Gustavo A. Mercier, Jr. MD,PhD Baylor University Medical Center Radiology American Radiology Associates 712 N. Washington, Suite 101 Dallas, TX 75246 214-826-8822 214-826-9792 fax gamercier|*|yahoo.com --0-411024957-1148518293=:34309 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi!

You may try Moldy. It is rigid body molecular dynamics program that uses a quaternion implementation for rotations. A google search should get you the web site.

Bye!
GMercier

"Eric Hu list.eric%gmail.com" <owner-chemistry|*|ccl.net> wrote:
Sent to CCL by: "Eric Hu" [list.eric_+_gmail.com]
------=_Part_24727_29052931.1148503596537
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Hi, I am conducting an organic molecular assembly simulation (about 55 atom=
s
in each subunit and there are 12 subunit in total). I want to freeze the
subunit internal vibration (saving sampling time) during md since I am more
interested in the assembly process between subunits.

Are there any suitable "rigid body" molecular dynamics packages for this
purpose? Thank you.

Eric

------=_Part_24727_29052931.1148503596537
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Hi, I am conducting an organic molecular assembly simulation (about 55
atoms in each subunit and there are 12 subunit in total). I want to
freeze the

subunit internal vibration (saving sampling time) during md since
I am more interested in the assembly process between subunits.



Are there any suitable "rigid body" molecular dynamics packages f=
or this purpose? Thank you.




Eric


------=_Part_24727_29052931.1148503596537--








--
Gustavo A. Mercier, Jr. MD,PhD
Baylor University Medical Center
Radiology
American Radiology Associates
712 N. Washington, Suite 101
Dallas, TX 75246
214-826-8822
214-826-9792 fax
gamercier|*|yahoo.com 
--0-411024957-1148518293=:34309--