Subject: Dendrimer MD/MM, Coordinates.

From: [email-masked] (Gustavo A. Mercier, Jr.)
Date: Wed, 10 Apr 1996 11:23:36 -0500

Hi!

I am interested in MD/MM of dendrimers. I have a few questions since I am a
neophyte in this area :(. Specifically, I am looking for software/algorithms
that people may use to generate coordinates and perform these
simulations. As described below, common programs like amber and charmm
have their limitations when applied to these molecules.

Although I have some experience with programs like amber and charmm,
it is clear that these programs expect linear polymers. Unfortunately,
the starbust dendrimers of PAMAM are branched polymers with two
branches off the tail end.
                                          /
                    C ------------N
                  /                      \
     -C-----N
                 \                      /
                    C-----------N
                                        \

So, when you have a repeating unit like
               /
-C------N
               \

and try to specify the sequence you need a mechanism to tell the program
that two residues are attached to one! In amber the link program does not
allow for this, nor the sequence command allows for this under charmm.
A potential work around can be develop using patches in charmm.

In principle this means that you could start your sequence from generation g0,
that is, with a core and its first branches, then patch along to add the
repeating units.
                                              /
                          C----------N
                        /            /       \
core =         N---C---N
                       \            \          /
                          C-------------N
                                                 \

Have two patches, one for each branch point along the N's. Then loop again
moving to the next set of "residues". The looping mechanism is tricky, but
can be simplified by specifying the branches of the core using the segid,
and each repeating unit by a residue number. If the RTF has internal
coordinates specified, this can be used to generate coordinates!
(Thanks to Dr. Langley for reminding  me of charmm patches!)

Has anybody implemented this in a charmm script and is willing
to share it?

Is there another, possibly simpler solution using other software or
even within charmm.

Thanks for your help!

Bye

Gustavo A. Mercier, Jr. M.D.-Ph.D.
NIH - LDRR
OD OIR LDRR
Building 10 Room B1N256
10 Center Dr MSC 1074
Bethesda, Maryland 20892-1074
phone: 301-402-3586, 301-496-1981
fax:      301-402-3216
e-mail: [email-masked]

>From [email-masked] Wed Apr 10 12:08 EDT 1996
Date: Wed, 10 Apr 1996 18:09:59 +0100
To: [email-masked]
From: [email-masked] (Fred Brouwer)
Subject: conference announcement update
Content-Length: 3226
Status: R

                     CONFERENCE

        MOLECULAR MODELLING OF CHEMICALS AND MATERIALS

         Amsterdam, The Netherlands, 9-10 September, 1996

Society's demands for affordable chemicals and materials with novel or
enhanced performance characteristics continue to grow as exciting new
application areas are recognised, and the requirements in existing areas
become increasingly more stringent. Molecular modelling and simulation
techniques have an important role to play in these developments by helping
to provide a more focussed, molecular-level understanding of chemical
products and processes, which in turn can help to guide future experimental
work. This meeting, organised by the Molecular Graphics and Modelling Society
and the University of Amsterdam, will bring together theoreticians and
experimentalists from a variety of relevant fields to discuss molecular
modelling approaches in chemicals and materials research, and is expected to
be of value to scientists in industry and academe alike. Topics covered by
the meeting will include:

 - Catalysis and Surfaces
 - Fluids and Interfaces
 - Polymers

Speakers will include:

Prof. E.J. Baerends (Amsterdam), Prof. J.H.R. Clarke (UMIST), Dr. J. Gale
(London), Prof. W.A. Goddard (Caltech), Dr. F. Muller-Plathe (ETH, Zurich),
Prof. K. Roberts (Strathclyde), Prof. R. Van Santen (Eindhoven),
Dr. B. Smit (Shell) and Prof. D. Tildesley (Imperial, London)

Organising Committee : Dr. M.A. King (Shell) Chairman; Dr. E.A. Colbourn
(Oxford Materials Ltd.); Dr. M.G.B. Drew (University of Reading);
Dr. A.M. Brouwer (University of Amsterdam) Local Organiser;
Dr. R. Peschar (University of Amsterdam) Local Organiser

Program

The program will consist of invited lectures and oral presentations. On
both days there will be a session of ca. three hours which will include
buffet lunch, poster session and a commercial exhibition, all in the same
location. Abstracts (one page A4, ready for reproduction) of contributed
talks or posters should be sent to Dr. A.M. Brouwer at the address below.
If you wish to present your work orally please ensure that your abstract
is in our possession before July 1, and please add a brief description of
your position and scientific career. The selection of oral presentations
will be made before July 30. The committee will favour contributions from
younger scientists.

Registration

The conference fee is DFl. 300 for regular participants, DFl. 175 for
students. For registration after July 1 the fee is increased by DFl 50.
To qualify for the reduced rate students must include a letter from their
research supervisor. A limited number of student bursaries will be available.
The registration fee includes a book of abstracts, lunches, coffee and tea
during breaks, and an informal dinner on monday evening.

Registration and hotel reservation forms are available at the:

Conference WWW page: Http://krop.chem.uva.nl/mgms/

or will be sent upon request at the (E-mail) adress below.

Send abstracts and registration form to:

Dr. A.M. Brouwer
University of Amsterdam, Laboratory of Organic Chemistry
Nieuwe Achtergracht 129, NL-1018 WS Amsterdam, The Netherlands
Fax  31 (0)20 5255670, E-mail: [email-masked]

>From [email-masked] Wed Apr 10 21:37:00 EDT 1996
From: "Wayne Huang" <[email-masked]>
Message-Id: <[email-masked]>
Date: Wed, 10 Apr 1996 17:23:47 -0700
Reply-To: [email-masked]
To: [email-masked], [email-masked]
Subject: 96.06.12 Computational Chemistry Workshops

Hello all,

Workshop time again! We are continuing to offer three-day intensive
Computational Chemistry Workshops to our chemistry community.
Due to the popular demand on June workshop, I have scheduled a second
workshop in June (June 26-28), in addition to the one in June 12-14.
Drop me a line at [email-masked] for a complete brochure.

Meanwhile, happy computing!

--Wayne

Attachment is the information on the workshop and course materials.
The complete brochure can be sent via fax/mail upon request.
======================================================================

		------------------------------------
		| COMPUTATIONAL CHEMISTRY WORKSHOP |
		------------------------------------

Intensive 3-day workshops focus on application of modern electronic
structure methods to chemistry. Lectures will describe underlying
theory, assess performance of modern electronic structure methods,
outline practical strategies for doing calculations, and illustrate
results of applications to diverse chemical problems. Laboratories
provide hands-on experience using a wide selection experiments, as
well as ample time to explore your own chemistry. Visualization and
animation will also be presented for both educational demonstration
and research presentation.

Here are the summary of workshop information:

_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/
_/                                                                _/
_/                    COMPUTATIONAL CHEMSITRY WORKSHOPS           _/
_/						                  _/
_/ Format:      3-day intensive workshop on electronic structure  _/
_/              methods and applications, and hands-on molecular  _/
_/              modeling laboratory on individual workstations.   _/
_/              It will provide:                                  _/
_/							          _/
_/		 o Concise summary of modern electronic structure _/
_/                 methods                                        _/
_/		 o Assessment of range and performance of their   _/
_/		   applications					  _/
_/		 o Hands-on experience in molecular modeling      _/
_/		 o Graphical Analysis of results                  _/
_/		 o Visualization and animation of structures and  _/
_/		   reactions 					  _/
_/							          _/
_/ Schedule:	June Workshop (1):      June 12-14, 1996          _/
_/		June Workshop (2):	June 26-28, 1996	  _/
_/              September Workshop: 	September 4-6, 1996       _/
_/              November Workshop:      November 6-8, 1996        _/
_/								  _/
_/ Instructors: Lecture Section - Dr. Warren Hehre		  _/
_/              Lab Section     - Dr. Wayne Huang		  _/
_/								  _/
_/ Location:    Wavefunction, Inc. Irvine, California, USA	  _/
_/								  _/
_/ Fee:         $1000 (50% off for academics, $500), which        _/
_/		includes course registration, five computational  _/
_/		textbooks and one animated CD-ROM, all breakfasts _/
_/		and lunches.  			                  _/
_/								  _/
_/ Textbooks:	o "Chemistry with Computation", Warren Hehre &	  _/
_/                Wayne Huang, 1995.				  _/
_/								  _/
_/		o "A Laboratory Book of Computational Organic     _/
_/		  Chemistry", Warren Hehere, Alan Shusterman &    _/
_/                Wayne Huang, 1996.				  _/
_/								  _/
_/		o "Experiments in Computational Organic Chemistry"_/
_/                Warren Hehre, Lonnie Burke, Alan Shusterman and _/
_/    		  William Pietro, 1993.				  _/
_/								  _/
_/		o "A Short Course in Modern Electronic Structure  _/
_/  		  Methods", Warren Hehre, 1995.			  _/
_/								  _/
_/		o Educational CD-ROM "SpartanLive - Visualization _/
_/		  of Chemical Structures and Reactions", Tom Hehre_/
_/		  Lonnie Burke, Wayne Huang & Warren Hehre, 1995. _/
_/								  _/
_/		o "Practical Strategies for Electronic Structure  _/
_/		  Calculations", Warren Hehre, 1995.		  _/
_/								  _/
_/ Information: Workshop WWW: http://www.wavefun.com/workshop.html_/
_/		or contact Wayne Huang for further information    _/
_/		including detailed brochure and course curriculum._/
_/              Tel: (714)955-2120 Fax: (714)955-2118	          _/
_/              E-mail: [email-masked]		          _/
_/							          _/
_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/_/