Subject: Pronunciation of "Conformer"

From: [email-masked] (Jesse Salb)
Date: Sat, 16 Mar 1996 00:43:36 GMT

I apologize for wasting valuable bandwidth, but is the preferred
pronunciation of "conformer"  either "con' form er"
or "con form' er"?

Thanks.

>From [email-masked] Tue Mar 12 03:30 EST 1996
From: Peter Grootenhuis <[email-masked]>
Subject: MD of non-globular proteins - answers
To: [email-masked]
Date: Tue, 12 Mar 1996 09:29:44 +0000 (WET)
Name: P.Grootenhuis
Organisation: NV Organon 
Phone: (+31)0412-661920
Content-Length: 5036
Status: RO

CCL-ers,

My original questions concerned MD of non-globular proteins where I observed
both in gas-phase and aqueous simulations a rather strong tendency of the 
system to adopt conformations that result in more globular shapes. 
Questions:
(1) Is anybody aware of (published) MD simulations of non-globular proteins ?
(2) Does anybody has (preferably computationally inexpensive) suggestions on 
	how to handle such a system ? 

Thanks for your suggestions! Here is a summary:
-------------------------------------------------------------------------------
From: [email-masked] (Soaring Bear)

	Sounds like you ought to use more gentle methods, like
lower temp, ramp gradient, shorter times, higher dielectric.
-------------------------------------------------------------------------------
From: Willy Wriggers <[email-masked]>

The problems you mentioned have also been observed by us. We carry  
out MD simulations of calmodulin, a dumbbell shaped protein of only  
148 aa residues, in solution (see "calmodulin" on my homepage at  
http://www.ks.uiuc.edu/~wriggers/). Earlier simulations by our  
collaborators at CUNY (see Pascal-Ahuir, Mehler, Weinstein: Molecular  
Engineering 1, 231-247, 1991 for review) had a limited solvent model  
(only explicit surface waters) and it could not be ruled out that  
observed structural changes were caused by the protein "sticking it's  
tongue out" of the water molecules, which tend to diffuse to the  
center of the protein.
The way we solve the problem now is by placing the protein in a 44 A  
radius sphere of water, which brings the total system size to 33,000  
atoms. Since the explicit solvent model and salt ions slow down the  
movement of calmodulin's domains, we need to simulate for 3 ns. I  
know such a calculation may not be feasible in every case. If you  
have limited resources, it's better to simulate only parts of the  
protein which are of interest, i.e. use stochastic boundary  
conditions (Brooks, Karplus, Pettitt: Proteins. (1988) Wiley  
Interscience Pub.). I would not recommend using a distance-dependent  
dielectric constant to model the solvent because it gives you the  
wrong electrostatics. Depending on your problem, you may also want to  
look at other newer "in vacuo" simulation techniques which use  
constraints (Collins, Burt, Erickson: Flap opening in HIV-1  
protease... (1995) Nature Struct. Biol. 2:334-338). 
-------------------------------------------------------------------------------
From: [email-masked] (Howard Alper)

  In your simulations, how do you treat the nonbonded interactions.  In
particular, do you use switching functions?  The reason I ask is that
while these functions do smooth away discontinuities in the energy, they
can create artificial maxima and minima in the interatomic, interresidue,
or intermolecular forces that could trap the particles at particular
separations from each other.  This can be seen by looking at the way the
switching function varies in the region where it goes from 1 to 0, and
considering what the derivative of the function would look like.
  I have seen this for simulations of neat water (K. Lau. H. E. Alper,
T. Thacher, and T. R. Stouch, J. Phys. Chem. 98, 8785 (1994)), as well as
in simulations of lipid bilayer systems.  Switching functions can decrease
the degree of motion a system undergoes, compared to other cutoff methods...
-------------------------------------------------------------------------------
From: Vincent Collura <[email-masked]>

I am not surprised about " a tendency" to fold into a globular (more compact)
shape in the gas-phase, the reason is certainly the electrostatics term of the
nonbonded energy. The best is to increase the dielectric constant (distance
dependent or not in your case?) close to the value of water. In your case, it
will be a good approximation because if it is not globular or compact it can be
deduced that it has certainly a substantial part of the surface in contact with
the solvent unless it is a membrane protein.
I am slightly more surprised that you observed this effect with the explicit
description of the solvent. Normally it should be more "rigid". If it is not a
compact protein ( higher % of hydrophilic residues? Is there a well defined
hydrophobic core in your protein ?) it is normal that it undergoes larger
average fluctuation at room temperature in the solvent, but it should'nt lead
to a more compact protein. Are you using Periodic Box conditions or only a
water shell around the protein ?
Have a look in the way the electrostatics terms are parameterized in your force
field....
 ______________________________________________________________________________
 Dr. Peter D.J. Grootenhuis       |
 N.V. Organon / CMC Dept. RK2337  | Phone  : +31-412-661920
 P.O. Box 20 / 5340 BH Oss        | Fax    : +31-412-662539
 The Netherlands                  | E-mail : [email-masked]
 _________________________________|____________________________________________

>From [email-masked] Tue Mar 12 12:54 EST 1996
From: "Gerald Loeffler" <[email-masked]>
Date: Tue, 12 Mar 1996 18:52:13 +0100
To: [email-masked]
Subject: OFF Files and MD
Content-Length: 1549
Status: RO

Hi!

In the manual for LEAP, a program used to setup systems for MD calculations
that came with our AMBER-distribution from Oxford Molecular, I read about OFF
(Object File Format). It says there:

	OFF is a general file format developed for LEAP...
	It is intention that future versions of AMBER and SPASMS will read
	this OFF file, rather than topology and coordinate files, for input
	data to molecular mechanics calculations.

So OFF should contain all the information about a chemical system that is
needed to start a MD simulation of that system: connectivities (topology),
force-field parameters, positions and velocities of the atoms - but not the
characteristics of the MD-simulation itself (as I understand it!).

Before I start worrying about OFF at all, I would really like to know:

	1) When will there actually be a MD-program that understands OFF?
	2) Will OFF only be supported by AMBER (and SPASMS) or is there a
	   chance that other MD-programs (CHARMM, discover) will read OFF.
	3) Is there a (definitive) specification of OFF somewhere.
	4) Is there any other movement towards a universal file-format for
	   the specification of chemical systems for MD-simulations?

Thanks a lot for your attention!
-gerald

--
Gerald Loeffler
PhD student in Theoretical Biochemistry

EMail: [email-masked]
Phone: +43 1 40480 612
Fax:   +43 1 4028525
SMail: University of Vienna
       Institute for Theoretical Chemistry
       Theoretical Biochemistry Group
       Waehringerstrasse 17/Parterre
       A-1090 Wien, Austria

>From [email-masked] Fri Mar  8 06:53 EST 1996
From: "Alicia Martinez Puebla" <[email-masked]>
Date: Fri, 8 Mar 1996 12:56:07 +0100
To: [email-masked]
Subject: Gaussian Workshop at Barcelona on 30-31 May
Content-Length: 4339
Status: RO

 With the sponsoring of Cray Research, Inc. Spain,
 Centre de Computacio i Comunicacions de Catalunya (C4)
 and Universitat de Barcelona announce

 INTRODUCTION TO GAUSSIAN:  THEORY AND PRACTICE

 Date: May 30 - 31

 Location: Centre de Supercomputacio de Catalunya (CESCA)

 Cray Research Spain is pleased to sponsor "Introduction to Gaussian:
 Theory and Practice."  The workshop will cover the full range of methods
 available in the Gaussian package with emphasis on new methods and
 features which make Gaussian applicable to an ever widening spectrum of
 questions.

 The workshop is structured to provide an introduction to electronic
 structure theory as well as a hands-on review for researchers, students,
 and scientists in industry.  The workshop will have emphasis on
 performance and utilization of Cray Research, Inc. supercomputers.
 In addition, practical strategies for doing CASSCF calculations will be
 presented.  Prof. Robb will discuss new CASSCF features along with some
 practical examples for planning and executing a CASSCF study.
 The language of the workshop is English.

      Instructors:

        Prof. Michael Robb                  King's College London
        Dr. Carlos Sosa                     Cray Research, Inc.
        Prof. Juan J. Novoa                 Universitat de Barcelona
        Mrs. Alicia Martinez                CESCA
        Dr. Jose L. Andres                  Universitat de Girona

      Tentative Agenda Topics:

        Introduction to Electronic Structure Theory

        Building Gaussian Input Decks
        Simple Model Chemistries
        SCF Methods (RHF/UHF/ROHF, GVB, MCSCF)
        Geometry Optimization Techniques
        Electron Correlation Methods
        Density Functional Theory Methods
        Thermochemistry via Model Chemistries
        Interpretation of Results and Molecular Properties
        Solvent Effects on Molecular Electronic Structure
        Gaussian Utilities
        Gaussian Performance on Cray Research Supercomputers &
        Estimating Resource Requirements

      The workshop will run from 9:00 AM to 1:00 PM and from 3:00 PM to
      7:00 PM.  Tentatively, lectures will run from 9:00 AM to 11:00 AM
      and 3:00 PM to 5:00 PM and Labs from 11:10 PM to 1:00 PM and from
      5:10 to 7:00 PM.  There will be 10 minutes recess between lectures.

 Additional hands-on sessions will be available. Workshop participants
 will be provided with access to the Cray to complete exercises,
 experiment and/or conduct short research topics. Each workshop
 participant will also be provided a copy of the Gaussian 94 User's
 Reference and a copy of Exploring Chemistry with Electronic Structure
 Methods.

 APPLICATION PROCEDURE

 All applicants must submit the attached application form and a cover
 letter which briefly (one or two paragraphs) describes your current
 research and how participating in this workshop will enhance it. The
 cover letter should also include one or two sentences indicating your
 level of experience with computers. Seats are limited (max. 20) and
 the potential applicants are encouraged to send the application material
 ASAP.

 Costs:

 Workshop registration:

    Academic - 17000 ptas        Commercial/Private - 25000 ptas
    Students may apply for the 3 scholarships that will be awarded

 Hotel accomodations: A list of hotel accomodations in the vicinity
 of the CESCA facility will be made available to all registrants.
 Room reservations will be the responsibility of each participant.

 Meals:  Meals will be the responsibility of each participant.

 PLEASE RETURN YOUR APPLICATION MATERIALS TO:

        [email-masked]

       (From where additional information can also be obtained)

 DEADLINES:

        Receipt of Registration Materials:      May 1, 1996

 -----------------------------------------------------------------------

 APPLICATION FORM:

 Name:

 Affiliation:

 Address:

 Telephone:

 Facsimile:

 E-Mail Address:

 Please indicate your Research Standing (check one):

 Faculty _______    Postdoctorate _______   Graduate Student ______
 Undergraduate Student _______   University Research Staff _______
 University Non-Research Staff ______  Government _______
 Industrial  ______  Other ______

 Remember to include the cover letter with the additional information.

>From [email-masked] Mon Mar 11 11:52 EST 1996
Date: Mon, 11 Mar 96 12:07:47 -0500
From: [email-masked] (Michael Moller)
To: Hiroshi Ogura <[email-masked]>
Subject: Re:  CCL:Making a crystal packing model in a computer
Cc: [email-masked]
Content-Length: 578
Status: RO

Dear Hiroshi,
The commercial product ChemPlus, from Hypercube, Inc. has
a crystal builder module which allows you to create a crystal
in HyperChem by defining the unit cell.

For more information, send e-mail to [email-masked] or look
at our home page:  http://www.hyper.com

Regards,
Michael
------------
Michael Moller, PhD
Email to: [email-masked]

Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040
http://www.hyper.com    Info: [email-masked]    Support: [email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]

>From [email-masked] Fri Mar  8 00:34 EST 1996
Date: Thu, 7 Mar 96 21:34:29 PST
From: "S. Park" <[email-masked]>
To: [email-masked]
Subject: free molecular mechanics code?
Content-Length: 454
Status: RO

Hello,

I would like to learn molecular mechanics by trying publicly available codes
with some data.  Could anyone kindly tell me where I could find simple (free)
codes that I can start with?  Specifically, I would like to have some
experience on force field calculation and I wonder if there are ftp
sites (web sites) where I could find parameters for the calculation.
Thank you very much for your time!

Regards,
Seongbin Park ([email-masked])

>From [email-masked] Tue Mar 12 10:02 EST 1996
Date: Tue, 12 Mar 96 09:57:59 -0500
From: Joel Polowin <[email-masked]>
Organization: Hypercube, Inc.
To: [email-masked], [email-masked]
Subject: Re: ccl: C60 multiple moments
Content-Length: 1184
Status: RO

> From: [email-masked]
> Date: Tue, 27 Feb 96 14:41:55 -0200

>  I tried to calculate the electronic structure of this
> molecule with my own CNDO program using the example from the
> HyperChem. These calculations give the non zero dipole moment
> for C60. Another hand on a symmetry considerations the first
> non zero moment of the molecule must be of 6th order. So my
> questions are:
>  1.  Why the dipole moment obtained with both in my CNDO
> version and HyperChem CNDO for C60 is non zero?
>  2.  Does anybody knows any calculations of electrical moments
> for C60?

When I optimize C60 with CNDO with HyperChem and calculate its dipole 
moment, I get the expected 0 dipole.  I do not know why your result
differs, but it seems to me that the most likely cause is that your 
structure is not optimized and not symmetrical.

Joel
------------
Joel Polowin, Ph.D.   Manager, Scientific Support
Email to: [email-masked]

Hypercube Inc, 419 Phillip St, Waterloo, Ont, Canada N2L 3X2 
(519)725-4040
Info requests to: [email-masked]    Support questions to: 
[email-masked]
Email group: Send "subscribe hyperchem" to [email-masked]
WWW: http://www.hyper.com/