From owner-chemistry@ccl.net Fri Jan 9 07:32:00 2009
From: "Tamas Gunda tgunda2-*-puma.unideb.hu" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Mol2Mol 5.6.1 available
Message-Id: <-38404-090108145734-15486-LcGpFIc45uGYSkfShCiqtw~~server.ccl.net>
X-Original-From: "Tamas Gunda" <tgunda2(a)puma.unideb.hu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
format=flowed;
charset="iso-8859-2";
reply-type=original
Date: Thu, 8 Jan 2009 20:16:41 +0100
MIME-Version: 1.0
Sent to CCL by: "Tamas Gunda" [tgunda2+/-puma.unideb.hu]
Dear CCL Members,
A new 5.6.1 service version of the molecule file conversion,
manipulation and utility program Mol2Mol is now available
> from http://www.gunda.hu/mol2mol as trial or shareware
version.
The current version of Mol2Mol recognizes, and interconverts
about 50 different file formats (including subtypes). By entering
a format string practically every Cartesian or MOPAC type Z matrix
formats can be in/outputted (even in polar coordinates).
You can even copy/paste coordinates from e-mails and display
them in Mol2Mol using the automatic recognition feature or using a
format string.
It can slice multiple structural files to single ones (such
as PDB models or MDL SD files to single ones) and vice versa
in several variations. Support for PDB Chime subformat
(with 1-2-3 bonds). Many molecular utilities.
Mol2mol is a very handy set of tools for everybody dealing with
molecular modelling.
It is impossible to write here all of the features of Mol2Mol,
but have a look at its home page:
http://www.gunda.hu/mol2mol
e-mail: mol2mol {at} gunda {dot} hu
POV-Ray fans may also have a look at the "desktop images" section
at the above adress or:
http://dragon.unideb.hu/~gundat/povraya.htm
The program is available as 30 days unrestricted trial version or
as shareware version.
From owner-chemistry@ccl.net Fri Jan 9 08:14:01 2009
From: "Alberto Otero de la Roza alberto||carbono.quimica.uniovi.es" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: CRITIC: program for QTAIM analysis in solids
Message-Id: <-38405-090109041737-25158-5XbS3XDiYTqxKukhpZvAbw]-[server.ccl.net>
X-Original-From: "Alberto Otero de la Roza" <alberto . carbono.quimica.uniovi.es>
Date: Fri, 9 Jan 2009 04:17:31 -0500
Sent to CCL by: "Alberto Otero de la Roza" [alberto##carbono.quimica.uniovi.es]
Dear CCL list,
We have developed critic, a new code for the topological (QTAIM)
analysis of the electron density in periodic solids. In this first
version, we have tried to provide the basic capabilities for a full
Atoms in Molecules study. A brief description of the features of
critic is:
* It can read the electron density from several sources, including
WIEN2k calculations (http://www.wien2k.at/) and PI calculations
(1).
* Fast and completely automatic localization of the critical points
(CPs) in the unit cell. Using the symmetry information provided in
the struct file, the irreducible wedge of the Wigner-Seitz cell is
calculated, and used to place the seeds for a Newton-Raphson
algorithm. The complete list of CPs is presented in the output,
along with their properties (density, laplacian,...). The
localization of all the CPs is usually completed within seconds to
minutes.
* Atomic basin integration using a quadrature scheme plus a bisection
strategy.
* Lots of ways of representing the density, laplacian and gradient
vector field: 1d, 2d, 3d, contour plots, basin plots, 2d and 3d maps
of flux lines,... These capabilities are enhanced by the use of
external graphical programs, with which critic interfaces: gnuplot,
geomview (http://www.geomview.org/), tessel
(http://web.uniovi.es/qcg/tessel/tessel.html),...
* Critic is publicly available under the GPL licence. It has been
published recently together with an article in Computer Physics
Communications (2), and is downloadable from the CPC library or upon
request to us.
(1) M.A. Blanco, A. Martn-Pends, V. Luaa, Quantum mechanical cluster
calculations of ionic materials: Revision 10 of the ab initio
Perturbed Ion program, Comput. Phys. Comm. 103 (1997) 287--302.
(2) A. Otero-de-la-Roza, M.A. Blanco, A. Martn-Pends and Vctor
Luaa, Critic: a new program for the topological analysis of
solid-state electron densities, Comput. Phys. Comm. 180 (2009)
157--166.
We are currently working in a new version of critic (critic2) where we
intend to implement lots of new features such as the use of different
scalar fields (laplacian, ELF, electrostatic potential, etc.), the
possibility of reading the electron density from a wider range of
sources,... This new code is not ready for public distribution. If you
are interested in the implementation of any particular feature, please
contact with us.
Therefore, the development of this first version of critic is frozen,
limiting to bug fixes and small updates. However, we will gladly
provide the users of critic with technical support, and we would
appreciate very much any comment about the program.
Best wishes,
Alberto
From owner-chemistry@ccl.net Fri Jan 9 09:53:01 2009
From: "amine amine m-22!A!hotmail.fr" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: molecular mechanic in amber
Message-Id: <-38406-090109095221-989-eJ9s/Mp8/sWLLLm7VN7KNw(!)server.ccl.net>
X-Original-From: "amine amine" <m-22]|[hotmail.fr>
Date: Fri, 9 Jan 2009 09:52:17 -0500
Sent to CCL by: "amine amine" [m-22:+:hotmail.fr]
Hi
I want to do a MM Energy minimisation using amber:
is it correct like this??
sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
with this sander.in
initial minimisation prior to MD
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 5000,
ntb = 0,
igb = 0,
ntc = 2,
ntf = 2,
cut = 12,
/
else? why i can do this?
From owner-chemistry@ccl.net Fri Jan 9 16:29:00 2009
From: "Richard Tia richtiagh\a/gmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: transition states
Message-Id: <-38407-090109154016-8940-ZwLwkEEX84pIn/wNYsdY1A%a%server.ccl.net>
X-Original-From: "Richard Tia" <richtiagh(0)gmail.com>
Date: Fri, 9 Jan 2009 15:40:13 -0500
Sent to CCL by: "Richard Tia" [richtiagh]|[gmail.com]
Hi everybody,
Does any one knows the best way(step by step instructions) as to how to compute transition states of cycloaddition reactions using spartan'06 (windows version)?
Thanks
Richard Tia
Email: richtiagh~!~gmail.com
Department of Chemistry
KNUST, Kumasi
Ghana
From owner-chemistry@ccl.net Fri Jan 9 17:04:01 2009
From: "steinbrt===rci.rutgers.edu" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: molecular mechanic in amber
Message-Id: <-38408-090109115333-5133-7PsYfBPBEsHUvUKgHqKZRw*_*server.ccl.net>
X-Original-From: steinbrt^rci.rutgers.edu
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Fri, 9 Jan 2009 11:02:23 -0500 (EST)
MIME-Version: 1.0
Sent to CCL by: steinbrt^rci.rutgers.edu
Hi amine
> sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
that is the correct command (leave out the brackets around -O) assuming
sander is in your path. The minimized structure will appear as restrt and
energy info in mdout
> with this sander.in
>
> initial minimisation prior to MD
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 0,
> igb = 0,
> ntc = 2,
> ntf = 2,
> cut = 12,
> /
> else? why i can do this?
While this will do a minimization, in my opinion there is no need to do
5000 steps of steepest descent before CG. Any special reason you set ncyc
to such a high value? Also, 10000 minimization steps are a lot, normally
you dont see much change after say 500 or so even for biomolecules. If you
really need such an extremely well minimized structure, look into the use
of specialized minimizers such as implemented in ambers nmode program.
Kind Regards,
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
From owner-chemistry@ccl.net Fri Jan 9 17:38:00 2009
From: "Gustavo L.C. Moura gustavo()mercury.chem.pitt.edu" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: ECP Basis set for Europium
Message-Id: <-38409-090109164235-20817-zwkDwrlmTdzbO2VyndkGsA-x-server.ccl.net>
X-Original-From: "Gustavo L.C. Moura" <gustavo : mercury.chem.pitt.edu>
Date: Fri, 9 Jan 2009 16:42:31 -0500
Sent to CCL by: "Gustavo L.C. Moura" [gustavo\a/mercury.chem.pitt.edu]
Dear CCL Readers,
I am looking for a very small ECP basis set for europium that includes the 4f electrons/orbitals in the core.
I am aware of the MWB52 basis set, but it is too large for me (5s4p2d for the valence). I am looking for a smaller basis set for the valence.
I found the CEP-4G basis set for europium but it includes the 4f electrons/orbitals in the valence and complicates the calculation (the system becomes multiconfigurational). The ideal for me would be a CEP-4G like basis set without the f electrons/orbitals in the valence.
Thank you very much in advance.
Sincerely yours,
Dr. Gustavo L.C. Moura
Gustavo _ mercury.chem.pitt.edu
From owner-chemistry@ccl.net Fri Jan 9 18:14:00 2009
From: "Ross Walker ross=rosswalker.co.uk" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: molecular mechanic in amber
Message-Id: <-38410-090109132222-28139-+IUk4gajK2KHf0bqgDy4jw~!~server.ccl.net>
X-Original-From: "Ross Walker" <ross_-_rosswalker.co.uk>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
charset="Windows-1252"
Date: Fri, 9 Jan 2009 09:55:25 -0800
MIME-Version: 1.0
Sent to CCL by: "Ross Walker" [ross..rosswalker.co.uk]
Hi
You should probably take a look at the tutorials on the AMBER website:
http://ambermd.org/tutorials/
Particularly the first one which explains how to setup simulations in
sander, how to minimize and then how to run MD. It is also a good idea to
sign up to the AMBER mailing list
http://lists.ambermd.org/mailman/listinfo/amber and post questions specific
to the AMBER software there.
To answer your question you input file looks okay, assuming of course that
you want to do a minimization in gas phase. Note, AMBER's standard minimizer
works with SHAKE but will only take you so far towards a minimum before it
will quit with a LINMIN failure error which essentially means it can go no
further.
All the best
Ross
> -----Original Message-----
> From: owner-chemistry+ross==rosswalker.co.uk a ccl.net [mailto:owner-
> chemistry+ross==rosswalker.co.uk a ccl.net] On Behalf Of amine amine m-
> 22!A!hotmail.fr
> Sent: Friday, January 09, 2009 6:52 AM
> To: Walker, Ross
> Subject: CCL: molecular mechanic in amber
>
>
> Sent to CCL by: "amine amine" [m-22:+:hotmail.fr]
> Hi
> I want to do a MM Energy minimisation using amber:
> is it correct like this??
>
>
>
> sander [-O] -i mdin -o mdout -p prmtop -c inpcrd -r restrt
>
>
> with this sander.in
>
> initial minimisation prior to MD
> &cntrl
> imin = 1,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 0,
> igb = 0,
> ntc = 2,
> ntf = 2,
> cut = 12,
> /
> else? why i can do this?