From owner-chemistry@ccl.net Tue Aug 26 07:28:01 2014 From: "Billy McCann thebillywayne{:}gmail.com" To: CCL Subject: CCL: TINKER with cyclic amino acids and distance restraints Message-Id: <-50443-140825234420-17382-ZCu3eBnH8A98O2NDtLFodA:-:server.ccl.net> X-Original-From: Billy McCann Content-Type: multipart/alternative; boundary=089e013d0520ad98030501801d0d Date: Mon, 25 Aug 2014 23:44:08 -0400 MIME-Version: 1.0 Sent to CCL by: Billy McCann [thebillywayne|a|gmail.com] --089e013d0520ad98030501801d0d Content-Type: text/plain; charset=UTF-8 Russell, I have access to software which can specify which terms are missing from the force field. Feel free to send me a copy of your pdb file via my personal email. BW On Monday, August 25, 2014, Russell W Driver rwdriver a kaist.ac.kr < owner-chemistry-$-ccl.net> wrote: > > Sent to CCL by: "Russell W Driver" [rwdriver%%kaist.ac.kr] > Dear Computational Chemists, > > I am a new TINKER user running Windows executables on a standard desktop > PC. > I am having difficulty making .xyz files from the .pdbs of cyclic amino > acid foldamers using the pdbxyz executable. Is this because the > forcefields I am using (like MM2) lack parameters for these atom > connectivities (types)? > > I have gMOLDEN for Windows but preparing the structures that way doesnt > seem to help. > Can anyone recommend an way around this? Or care to pass along a > parameter patch for cyclic structures? > > Also, I would like to do calculations with distance and dihedral angle > restraints. Can anyone show me an example of a keyfile (?) that contains > script for dihedral angles and interatomic distance restraints? > Much appreciated! > > Best regards, > Russell > > Department of Chemistry > KAIST > rwdriver\a/kaist.ac.kr> > E-mail to subscribers: CHEMISTRY-$-ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST-$-ccl.net or use> > > -- Sent from a mobile device. Please forgive misspellings and/or brevity. --089e013d0520ad98030501801d0d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Russell,

I have access to software which = can specify which terms are missing from the force field. Feel free to send= me a copy of your pdb file via my personal email.=C2=A0
=

BW

On Monday, August 25, 2014, Russell W Drive= r rwdriver a kaist.ac.kr <owner-chemistry-$-ccl.net> wrote:
<= blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1px= #ccc solid;padding-left:1ex">
Sent to CCL by: "Russell W Driver" [rwdriver%%kaist.ac.kr]
Dear Computational Chemists,

I am a new TINKER user running Windows executables on a standard desktop PC= .
I am having difficulty making .xyz files from the .pdbs of cyclic amino aci= d foldamers using the pdbxyz executable.=C2=A0 Is this because the forcefie= lds I am using (like MM2) lack parameters for these atom connectivities (ty= pes)?

I have gMOLDEN for Windows but preparing the structures that way doesnt see= m to help.
Can anyone recommend an way around this?=C2=A0 Or care to pass along a para= meter patch for cyclic structures?

Also, I would like to do calculations with distance and dihedral angle rest= raints.=C2=A0 Can anyone show me an example of a keyfile (?) that contains = script for dihedral angles and interatomic distance restraints?
Much appreciated!

Best regards,
Russell

Department of Chemistry
KAIST
rwdriver\a/kaist.ac.kr=



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Sent from a mobile device. Please forgive= misspellings and/or brevity.
--089e013d0520ad98030501801d0d-- From owner-chemistry@ccl.net Tue Aug 26 08:56:00 2014 From: "Frederic Bohr frederic.bohr]_[univ-reims.fr" To: CCL Subject: CCL:G: Release 2014 of Kisthelp software Message-Id: <-50444-140826084834-30969-fM5E82kmxzNyHkwU2PAOww ~ server.ccl.net> X-Original-From: "Frederic Bohr" Date: Tue, 26 Aug 2014 08:48:32 -0400 Sent to CCL by: "Frederic Bohr" [frederic.bohr##univ-reims.fr] Dear all, We are pleased to announce the release Kisthelp2014. KiSThelP is a cross-platform free open-source program developed to estimate thermodynamic and kinetic properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, NWChem). Some key features are: - gas-phase molecular thermodynamic properties (offering hindered rotor treatment) - thermal equilibrium constants - transition state theory rate coefficients (TST, VTST) including one-dimensional tunnelling effects (Wigner and Eckart) - RRKM rate constants, for elementary reactions with well-defined barriers. For information, please visit: http://kisthelp.univ-reims.fr KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the GUI and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D-plots, exporting images and data files. These features make this program also well suited to support and enhance students learning and can serve as a very attractive courseware, taking the teaching content directly from results in molecular and kinetic modelling. Kindest regards, -- The KiSThelP developement team. ----------------------------------------------- Pr F. BOHR LISM EA 4695, Case No 18 UFR Sciences Exactes et Naturelles Moulin de la Housse BP 1039 51687 REIMS Cedex 2 France Tel. (phone): (0)3-26-91-32-33 ml (e-mail): frederic.bohr=-=univ-reims.fr ----------------------------------------------- From owner-chemistry@ccl.net Tue Aug 26 13:31:00 2014 From: "sudipta sudipta.mml]=[gmail.com" To: CCL Subject: CCL: Derivative of overlap integral for Slater orbital Message-Id: <-50445-140826123457-8150-PBr6OyQ3Gu1C2h2YNXcCKA]-[server.ccl.net> X-Original-From: sudipta Content-Type: multipart/alternative; boundary=089e01494210a6ea2005018ae14d Date: Tue, 26 Aug 2014 12:34:46 -0400 MIME-Version: 1.0 Sent to CCL by: sudipta [sudipta.mml[-]gmail.com] --089e01494210a6ea2005018ae14d Content-Type: text/plain; charset=UTF-8 Hi All, Does anyone have solution for the derivative of overlap integral for Slater orbital. For the sake of simplicity, I don't need the angular part of it. If anyone have solution or reference for the radial part of Slater orbital, please share with me. Thanks in advance Best Sudipta --089e01494210a6ea2005018ae14d Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi All,

Does anyone have solution f= or the=C2=A0 derivative of overlap integral for Slater orbital. For the sak= e of simplicity, I don't need the angular part of it. If anyone have so= lution or reference for the radial part of Slater orbital, please share wit= h me.

Thanks in advance

Best
Sudipta
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