From tripos!metis!matt@uunet.UU.NET Thu Oct 7 10:42:23 1993
From: tripos!metis!matt@uunet.UU.NET (Matt Clark)
Message-Id: <9310072142.AA06977@metis.UUCP>
To: uunet!ccl.net!chemistry@uunet.UU.NET
Subject: Re: conjugation in mol mech
Date: Thu, 07 Oct 93 14:42:23 EDT
Neil Ostlund makes an important point about atom types in
molecular mechanics, and how different bond types may occur
between two atom types.
The Tripos force field solves this problem by adding an extra
variable to the force field, the bond type. This applies in
particular to bond stretch and torsion terms.
This allows more flexibility in handling conjugated systems. The
single bond length between two sp2 carbons is about 1.47 Angstroms,
the double bond length is 1.33 Angtroms. There are different
torsion parameters for single and aromatic bonds used in the
case of biphenyl torsions, allowing these to be parametrized more
accurately. It isn't the same as a pi calculation, but significantly
improves the accuracy for conjugated systems.
I would encourage anyone developing new force fields to use this
idea; it greatly expands the possibilities for future expansion of
the force field. Organometallic modeling is much easier with
this scheme - you can assign different bond lengths for bridging
bonds, dative bonds etc., between the same two atom types.
From CTARG@Levels.UniSA.Edu.Au Sat Oct 9 01:25:44 1993
Date: Fri, 08 Oct 1993 15:55:44 +0930
From: CTARG@Levels.UniSA.Edu.Au
Subject: ionsiation potentials/electron affinities
To: chemistry@ccl.net
Message-Id: <01H3VIZGR9YQ9LVEEL@Levels.UniSA.Edu.Au>
Hi Netters,
The question I have to ask probably falls into the
category of simplistic rubbish that I should look up in a
school library somewhere but never mind....
I have been trying to reproduce the Gasteiger charge coefficients
as used by Chem-X with the view to parameterising some other atoms.
The reference paper 'Iterative partial equilization of orbital
electronegativity - a rapid access to atomic charges' by Gasteiger
and Marsili, Tetrahedron, vol36,(1980) pp 3219 to 3288 gives
the a parameter of the electronegativity polynomial as
a=1/2(I+E) where I is the ionisation potential and E is the
electron affinity. For Hydrogen the text value for a is given as
7.17 eV which is fine using literature values of I and E. However
I can't seem to reproduce any of the polynomial parameters for
any other atoms. The type of bonding to each atom is obviously taken
into account as different a, b and c coefficients are quoted for
different bonding arrangements. How is ionsiation potential of an ATOM
calculated/measured when it is bonded to something else?
Can somebody enlighten me as to how these values are arrived at?
Sorry about being so simple minded but somebody has to ask theses
questions to make everybody else feel good!
Thanks
Andy
From AJS1@phx.cam.ac.uk Fri Oct 8 12:37:26 1993
From: Anthony Stone <AJS1@phx.cam.ac.uk>
Message-Id: <9310081137.AA16677@fandango.ch.cam.ac.uk>
Subject: van der Waals radii
To: chemistry@ccl.net
Date: Fri, 8 Oct 1993 12:37:26 +0000 (BST)
A further issue in the context of van der Waals radii is that atoms in
molecules are not spherical, so one has to consider whether some sort of
spherical average is in fact appropriate, or whether the anisotropy needs to
be taken into account. The paper by Nyburg & Faerman in Acta Cryst B41 (1985)
274 gives an analysis of crystal packings that shows the anisotropies very
clearly. Sally Price and I have reviewed this issue, among others, in J. Phys.
Chem. 92 (1988) 3325.
Anthony Stone
University Chemical Laboratory, Internet: ajs1@phx.cam.ac.uk
Lensfield Road, Phone: +44 223 336375
Cambridge CB2 1EW Fax: +44 223 336362
From MVOUE%BNANDP51.BITNET@phem3.acs.ohio-state.edu Fri Oct 8 14:11:34 1993
Date: Fri, 08 Oct 1993 14:11:34 +0000 (N)
From: MVOUE%BNANDP51.BITNET@phem3.acs.ohio-state.edu
Subject: Solution of Oernstein-Zernicke equations
To: chemistry@ccl.net
Message-Id: <01H3VF85XYHE8WWOEJ@BNANDP51>
Dear Netters,
I was interested if anyone could help me to locate a program which will solve
the Oernstein-Zernicke equations for (poly-)electrolyte systems.
Any information is welcome.
Thanks in advance.
Michel Voue
Lab. Theoretical Biotechnology
University of Namur (Belgium)
bitnet%"MVOUE@BNANDP51"
From dirk@rulglj.LeidenUniv.nl Fri Oct 8 06:15:21 1993
Date: Fri, 8 Oct 93 13:15:21 -0700
From: dirk@rulglj.LeidenUniv.nl (Dirk Huckriede)
Message-Id: <9310082015.AA09000@rulglj.LeidenUniv.nl>
To: CHEMISTRY@ccl.net
Subject: Volume calculation
Hello netters,
I'm looking for a program which calculates the volume of a molecule, given
the atom types and their coordinates.
Can anyone help me ?
Bye !
Dirk Huckriede
Conformational Analysis Group
Gorlaeus Laboratories
Leiden University
P.O. Box 9502 Phone : +31 71 274505
2300 RA Leiden Fax : +31 71 274488
The Netherlands E-mail : dirk@rulglj.leidenuniv.nl
From crawdad@smerdis.ccqc.uga.edu Fri Oct 8 03:56:11 1993
From: crawdad@smerdis.ccqc.uga.edu (Daniel Crawford)
Message-Id: <9310081256.AA27060@smerdis.ccqc.uga.edu>
Subject: Re: Searching for Duke
To: chemistry@ccl.net
Date: Fri, 8 Oct 1993 08:56:11 -0500 (EDT)
The domain for information on Duke University is:
acpub.duke.edu
chemistry in particular is,
chem.duke.edu
Try getting information through those addresses and see if that helps.
-Daniel (Duke T'92)
--
T. Daniel Crawford Center for Computational Quantum
crawdad@smerdis.ccqc.uga.edu Chemistry
From young@slater.cem.msu.edu Fri Oct 8 03:53:09 1993
Date: Fri, 8 Oct 93 07:53:09 -0400
From: young@slater.cem.msu.edu (Dave Young)
Message-Id: <9310081153.AA15065@slater.cem.msu.edu>
To: chemistry@ccl.net
Subject: Fermi surface vs van der Waals surface
Subj: Fermi surface vs Van der Waals surface
There was recently a posting asking whether the fermi surface in
a solid state calculation is analogous to the van der Waals surface
in a molecular scheme.
The answer is NO!!
The Fermi surface is defined as the surface of all points in
k space with the Fermi energy. Here k is a measure of the amount
of bonding or antibonding character in a band (think MO for band, roughly).
This is not defined in physical space, so it has no analogous properties
to a Van der Waals surface.
If you would like an analogy for the Fermi surface, think of it
as the HOMO, where the Fermi energy is the energy of the HOMO orbital.
However, keep in mind that in solids there is a continum of states
defined by a band, thus several bands may cross the Fermi energy,
thus the HOMO can not be defined as ONE orbital.
Dave Young
young@slater.cem.msu.edu
youngdc@msucem
From msjones@whale.st.usm.edu Sat Oct 9 37:42:53 1993
From: msjones@whale.st.usm.edu (Michael Sean Jones)
Message-Id: <9310081726.AA20559@whale.st.usm.edu>
Subject: REGULATIONS
To: CHEMISTRY@ccl.net (chemlist)
Date: Fri, 8 Oct 1993 12:26:53 +22304916 (CDT)
Netters,
I am writing in response to a letter that we all received from Jan
Labonowski(spelling???). It stated that he/she would not allow messages
of the type "...searching for...", etc. to be broadcast on the list. This
seems illogical to me, since the whole purpose of the internet is to
improve and raise the efficiency of communications. In particular, this
list should serve as an extension of the purpose of the internet; that is,
to improve the efficiency of communications between scientists interested
in computational chemistry. This allows a very specialized list of
individulals to view the message. The messages, in fact, would not make
much sense to anyone outside of the computational chemistry field.
It is to the benefit of everyone involved with the list to allow such
communications as "...searching for..." to be posted. Sure, like Jan
stated in the letter, anyone could go to a library, even a high school
library, to find addresses of people around the world. However, very few
libraries will keep internet or bitnet addresses on file, as they change
very often, and would be too hard to keep up with. This is the very
reason why a successful "Internet White Pages" has yet to appear. Sure,
there are services available for finding file names, and people, but the
lists are kept for only a limited number of machines around the world.
Furthermore, as was stated earlier, the purpose of the internet is not
facilitate efficient information exchange. This list, being a part of the
internet, should respect the purposes of the internet by allowing such
messages.
It is easily understood why messages such as "... searching for an art
professor by the name of..." would be banned from the list, but the
searches I have seen have been relevant to the field of computational
chemistry. What a better group to ask for an address of a computational
chemistry researcher's address than this list?
I might also add, that even though Jan CRUDELY suggested that everyone
who did not want messages like that sent send me a message telling me not
to do it anymore on this list. Jan also mentioned that once I got 2000
messages, I might not do it anymore. Well Jan, such a suggestion goes
outside of even your own guidelines for the use of this list. Read the
rules. Even after the suggestion that everyone who did not want me to
send messages like that send me a message telling me not to, noone did.
Obviously, the VAST majority of the 2000 subscribers enjoy the ability to
ask colleagues for addresses. Maybe you should to.
I do enjoy the use of this list, but the guidelines seem to be
contradictory to the whole purpose of the internet. If anyone else feels
the way that I do, please subscribe to the list.
I might also suggest simply glancing at the name of the sender and the
subject of the message before reading it. Using ELM this is possible.
Then, if you are not interested in the message, simply delete it. It
works well for deleting messges that you do not know much about, such as
requests for addresses that that you do not know.
Mike
msjones@wave.st.usm.edu
From CHAMH@INDSVAX1.INDSTATE.EDU Fri Oct 8 09:34:00 1993
Date: Fri, 8 Oct 1993 14:34 EST
From: CHAMH@INDSVAX1.INDSTATE.EDU
Subject: Problem with MECI in MOPAC93
To: chemistry@ccl.net
Message-Id: <01H3VG67OV2C0017ER@INDSVAX1.INDSTATE.EDU>
I am running MOPAC93 on the RS/6000 and find that when I use MECI on a
system, the .out file builds up to a point (e.g. in the middle of the
Cartesian coordinates or interatomic matrix), and the job hangs.
The MECI (and related keywords) works fine for 'smaller' systems, but above
a certain number of atoms the above problem occurs. The problem is not
with DIMSIZES becasue larger systems work without MECI.
If anyone has experienced this problem and identified a workaround, or
otherwise has a suggestion for a fix, please contact me.
Many thanks,
Arthur M. Halpern
Department of Chemistry
Indiana State University
Terre Haute, Indiana
(812) 237-2182
BITNET: CHAMH@INDSVAX1
INTERNET: chhalp@scifac.indstate.edu
From adrian@silver.chem.nwu.edu Fri Oct 8 10:31:47 1993
From: adrian@silver.chem.nwu.edu (Adrian Roitberg)
Message-Id: <9310082031.AA08068@silver.chem.nwu.edu>
Subject: Extended Huckel
To: chemistry@ccl.net
Date: Fri, 8 Oct 93 15:31:47 CDT
Dear netters,
Does somebody out there know about extended huckel parameters for charged
Ru atoms ??
I have found them for neutral Ru, but need them for Ru(II) and Ru(III) if
possible.
Also, does Prof. Roald Hoffman have an e-mail address were to reach him ??
Thanks a lot.
Adrian E. Roitberg
=============================================================================
Dept. of Chemistry | Phone: (708) 491-3423
Northwestern University | Fax : (708) 491-7713
2145 Sheridan Road. Evanston, IL |E-mail:adrian@silver.chem.nwu.edu
60208-3113 |
=============================================================================
From arne@escher.mbi.ucla.edu Fri Oct 8 06:49:43 1993
Message-Id: <9310082049.AA01652@escher.mbi.ucla.edu>
To: msjones@whale.st.usm.edu (Michael Sean Jones)
Subject: Re: REGULATIONS
Date: Fri, 08 Oct 93 13:49:43 -0700
From: "Arne Elofsson (arne@uclaue.mbi.ucal.edu)" <arne@escher.mbi.ucla.edu>
I do not agree with (Michael Sean Jones)
Actually I think it is quite anoying to read all
these messages, Do you know the adress to ...
etc etc
Even if this is usefull it takes a lot of time
for the othr 1999 subscribers who not is interested
in finding the adress to prof X. I think there is a
huge difference between a mailing list and the use
of usenet archives. In these archives I search for the
kind of information I want, while in a mailing list
the information is forced onto after a subscription.
These mails are mixed up with all other (personal)
mails, therefore it is necessary to keep the number
of mails you get to a (rather) small number. You can
not get only 10 % interesting mails.
therefore I suggest:
Either
1. Use sci.chem or so for asking these questions
or.
2. Create another mailing list "comp-chem-where-are-you"
I'm sure Jan is willing to give away his scripts
for the mailinglist.
arne.
PS. another good (?) idea might be to set up a
FAQ available through ftp or mailserver, as the
same questions appear again and again, as people
not uses the excellent search routines. But I guess
this is a lot of work.
From JKONG@ac.dal.ca Fri Oct 8 15:23:44 1993
Date: Fri, 08 Oct 1993 18:23:44 -0300
From: JKONG@ac.dal.ca
Subject: Reply directly to the original sender?
To: chemistry@ccl.net
Message-Id: <01H3VO5Z07MA000MY2@AC.DAL.CA>
Dear netters,
A few days I used up my disk quota and I guess I missed some parts
of the discussions about reviewing/publishing and DFT and I should apologize
to some fellows who may get bounced messages.
Most of my files are mails. Most of the mails I get from this list
are replys to questions. I suppose the senders just type reply command to
answer. I usually use VAX/4500 to receive mails and the reply command
sends the message directly to the original sender. But I think on some
machines reply utility sends the message to the list and everybody gets a
copy. (Usually reply sends messages to the address at the fist line of
the message you are reading.)
I thought it would be better to send replies of technical questions
to the original sender instead of the list unless you think other people
will be interested too and the original sender is supposed to summarize the
replies in a few days. You can request the replies from the original
sender if you are interested in the topic.
How is that?
Jing
From WALKERG@cofc.edu Tue Oct 8 12:49:43 1993
Date: 08 Oct 1993 17:49:43 -0500 (EST)
From: WALKERG@cofc.edu
Subject: Working on Eley-Rideal modeling...
To: chemistry@ccl.net
Message-Id: <01H3VMUYUFVM006G5P@cofc.edu>
Organization: College of Charleston
Hi. I'm totally new to this list, so I'll keep this as brief as
possible. I'm an undergraduate at the University of Charleston working on
a research project in computational chemistry. The project is an attempt
to model and propose new theories about the Eley-Rideal mechanism for gas/
surface reactions. This post is merely an attempt to shake out anyone
working on similar problems. I could certainly use your advice.
-Gary E. Walker
Junior, University of Charleston
Charleston, SC
Walkerg@ashley.cofc.edu
From scott@paganini.biocad.com Fri Oct 8 05:23:46 1993
Date: Fri, 8 Oct 93 12:23:46 -0700
From: scott@paganini.biocad.com (Scott Kahn)
Message-Id: <9310081923.AA13196@paganini.biocad.com>
To: CHEMISTRY@ccl.net
Subject: United atom summary
Here is a summary of the responses received for my question on untied atoms.
Many thanks to all that relied!
*>> I would like to locate any/all references that discuss the derivation
*>> and/or calibration of united atom forcefield parameters, and would
*>> appreciate any help that those participating in this list can offer.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From dan@omega.chem.yale.edu
We use united atom force field parameters quite a bit.
Unfortunately they are not useful in all cases. We found that the
only way to get the proper free energy of hydration for benzene was
to use an all atom model; you cannot include charges on a 6 site
model due to the need to preserve the 6-fold symmetry of the
molecule. It's not so much of a problem.
Here's the reference for the OPLS force field for proteins:
The OPLS Force Field for Proteins. Energy Minimizations
for Crystals of Cyclic Peptides and Crambin.
W. L. Jorgensen and J. Tirado-Rives
J. Am. Chem. Soc., 110, 1657 (1988).
The current version of the parameter set has replaced the united atom
aromatic rings with all atom ones.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From wk01189@worldlink.com
In addition to the "classical" AMBER and OPLS references you may want
to look at the work of Dunfield et al. in Scheraga's lab describing UNICEPP
(J. Phys. Chem. 82, 2609 [1978]). It is one of the few cases I am aware
where they put some effort into trying to reproduce the all-atom version of
the potential function (in this case, ECEPP). Also, Hall and Pavitt in their
comparative study of different force fields found a hybrid version of UNICEPP
to be one of the most accurate (the reference is J.Comp.Chem. 5, 441-450
[1984]). It is unfortunate that Scheraga and co-workers did not keep up with
UNICEPP and almost never used in publications after the original description;
however, the group of N. Go in Japan (and his followers) have used this
potential function in a number of papers (some of the most recent in the
latest issue of Proteins).
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
From grootenhuis@akzo.akzo.400net.nl (Dr. Peter D.J. Grootenhuis)
I have a paper in press (in Molecular Simulation, it may be already out)
that is concerned with the parametrisation of a united atom representing
carbohydrate hydroxyl groups. The whole procedure is described in detail.
We call the approach CHEAT (Carbohydrate Hydroxyls represented by
Extended AToms). I hope it will be of use ...
------
Scott D. Kahn, BioCAD Corporation (415) 903-3917
Email : scott@biocad.com
From sslagle@silibio.ncsa.uiuc.edu Fri Oct 8 15:14:11 1993
Date: Fri, 8 Oct 93 20:14:11 -0500
From: sslagle@silibio.ncsa.uiuc.edu (Stuart Slagle)
Message-Id: <9310090114.AA03996@silibio>
To: chemistry@ccl.net
Subject: Re: regulations
Some individuals have voiced conflicting opinions regarding the
admission of "in search of ..." requests on this list. To state it simply,
the requests are highly bothersome. These requests reduce the signal to
noise on this mailing list. The amount of *crap* on this list is often
frustrating enough that I erase all mail from osc without reading them. By
avoiding the "in search of ..." requests, will someone on the net do my
library research for me requests, and the other inane posts on this group,
it is difficult to find the truly informative or thought provoking posts.
I have personally unsubscribed/resubscribed to this list multiple times for
this very reason. Only the announcements of new software keeps me on this
list. The question is for how long?
To Jan and Mike: please fight this out of the list.
To all: flame to me not the list -- please!
Stuart Slagle
U of Illinois@U-C
sslagle@ncsa.uiuc.edu
From mckelvey@Kodak.COM Fri Oct 8 09:26:26 1993
Date: Fri, 8 Oct 93 13:26:26 -0400
Message-Id: <9310081726.AA03687@Kodak.COM>
From: mckelvey@Kodak.COM
To: osc@Kodak.COM
Subject: MOPAC 6 on PC
We run it routinely...NDP compiler...33MHZ-486 = 12 % of 25MHZ RS6000
John McKelvey