From jkl@ccl.net Fri Jul 17 13:29:42 1992
Date: Fri, 17 Jul 1992 13:29:39 -0400
From: jkl@ccl.net
To: tchemistry@ccl.net
Subject: mopac.man postscript file?
Status: R
Posted to the list for:
= Date: Thu, 16 Jul 1992 9:07:27 -0700 (PDT)
= From: F0418950@JAGUAR.CSC.WSU.EDU
Does anyone have, or know where I can find a postscript version of
the mopac6.0 manual (the mopac.man file)? Whenever I print the mopac.man
file I have, the pages are shifted so I use up almost twice as much paper
as it should take (189 pages). I have tried various formaters and ported
it to ms word and wordperfect as well, but to no avail.
Thanks in advance,
Andrew
f0418950@jaguar.csc.wsu.edu
From jkl@ccl.net Fri Jul 17 13:38:09 1992
Date: Fri, 17 Jul 1992 13:38:06 -0400
From: jkl@ccl.net
To: tchemistry@ccl.net
Subject: Re: A Semiempirical Life
Status: R
Sent to the list for:
= Date: Thu, 16 Jul 1992 14:12:05 -0400
= From: hyper!slee (Thomas Slee) ,or slee@hyper.com
Following up Brian Duke's question: the task of giving semi-empirical
methods a firm theoretical grounding has been addressed by Karl Freed,
of the University of Chicago. It is likely that the paper Dr. Duke
recalls seeing in J. Chem. Phys. is one of Freed's. Freed does not to
my knowledge ask about the limitations of Hartree-Fock theory, however;
instead he argues that the essential approximation of semi-empirical
methods is the use of valence orbitals only. Freed shows that you can
write out an equation that yields the exact energies of the valence
states of the system in such a limited basis if you are prepared to use
an effective Hamiltonian that has many (more than two-) body
effective interactions. A recent review by Thiel (Tetrahedron, vol 44,
No 24, p 7393) summarizes the work briefly, and gives several of the key
references.
Freed's work does not seem to have had much in the way of practical
consequences that I have seen (and I may well be wrong, of course ... ). It
does suggest some ways forward in terms of writing out semi-empirical
Hamiltonians, but perhaps semi-empirical methods are not at a stage
where their structure can be directed by formal considerations.
Tom Slee, Hypercube
--
Tom Slee
Hypercube, Inc., #7-419 Phillip St., Waterloo, Ont. N2L 3X2
Internet: slee@hyper.com Tel. (519) 725-4040
From jkl@ccl.net Fri Jul 17 13:40:03 1992
Date: Fri, 17 Jul 1992 13:39:59 -0400
From: jkl@ccl.net
To: tchemistry@ccl.net
Subject: CHARMm .DCD READ/WRITE SELE ATOMS
Status: R
Sent to the list for:
= Date: 16-JUL-1992 18:37:57.27
= From: WSONNEN@EAGLE.WESLEYAN.EDU
This is a question for any CHARMm guru on the net.
I would like to create a trajectory file (.DCD file) from an
existing .DCD file. I want the new .DCD file to contain only
selected atoms from the entire coordinate set. I have tried
a number of variations without success. Any help would be
appreciated.
Below are two excerpts, each followed by the relevant CHARMm .LOG
output, from two files. As you can see i tried two commands: the
COOR READ and the TRAJ READ/TRAJ WRITE.
Thank you
Wayne Sonnen
wsonnen@eagle.wesleyan.edu
**************************************************************************
...........STUFF DELETED........................
OPEN READ UNIT 51 FILE NAME TEST.DCD
OPEN WRITE UNIT 52 FILE NAME DNA2.DCD
WRITE COOR UNIT 52 FILE
*
SET 1 1
LABEL LOOP
READ COOR UNIT 51 FILE IFILE @1
WRITE COOR UNIT 52 FILE
INCR 1 BY 1
IF 1 LT 2.5 GOTO LOOP
STOP
END
*******************LOG FILE FOR ABOVE STUFF:****************************
******************** ... STUFF DELETED ....................*************
CHARMM> OPEN READ UNIT 51 FILE NAME TEST.DCD
UNIT 51 OPENED FOR READONLY ACCESS TO TEST.DCD
CHARMM> OPEN WRITE UNIT 52 FILE NAME DNA2.DCD
UNIT 52 OPENED FOR WRITE ACCESS TO DNA2.DCD
CHARMM> WRITE COOR UNIT 52 FILE
RDTITL> *
RDTITL MESSAGE: NO TITLE READ.
CHARMM>
CHARMM> SET 1 1
Parameter # 1 set to "1"
CHARMM> LABEL LOOP
CHARMM> READ COOR UNIT 51 FILE IFILE @1
RDCMND substituted parameter 1: "1"
SPATIAL COORDINATES BEING READ FROM UNIT 51
TITLE: * SCRIPT FILE PRODUCED BY QUANTA
TITLE: * DATE: 5/24/92 13:47:40 CREATED BY USER: quanta
TITLE: *
READING FROM COORDINATE TRAJECTORY, IFILE = 1
** WARNING ** MULTIPLE COORDINATES FOR
****
**NOTE: AFTER GRNERATING THIS STUFF THE MACHINE JUST 'HUNG'************************************************************
****
SECOND FILE:
***********************************************************************
.....STUFF DELETED.........
OPEN READ UNIT 51 FILE NAME TEST.DCD
OPEN WRITE UNIT 52 FILE NAME DNA2.DCD
TRAJ IREAD 51 IWRITE 52
*
SET 1 1
LABEL LOOP
TRAJ READ SELE BYNUM 1:542 END
TRAJ WRITE SELE BYNUM 1:542 END
INCR 1 BY 1
IF 1 LT 2.5 GOTO LOOP
STOP
END
**************LOG FILE FOR THIS RUN: THE "SELE ... " IS NOT ALLOWED***
.....STUFF DELETED.........
CHARMM> TRAJ WRITE SELE BYNUM 1:542 END
TRAJ: WRITING NEXT TRAJECTORY FILE, OPTIONS;
SKIP= 500 NPRIV= 15500 NSTEP= 25000 TRAJU= 52
**** Warning **** The following extraneous characters
were found while command processing in CHARMM
SELE BYNUM 1:542 END
CHARMM> INCR 1 BY 1
Parameter # 1 set to "2"
****************************************************************
From jkl@ccl.net Fri Jul 17 13:41:45 1992
Date: Fri, 17 Jul 1992 13:41:41 -0400
From: jkl@ccl.net
To: tchemistry@ccl.net
Subject: Relativistic HF Basis Sets
Status: R
= Date: Fri, 17 Jul 92 10:12:05 -0500
= From: perkins@tc4.fi.ameslab.gov (Leslie S. Perkins)
Dear Colleague,
I am looking for relativistic Hartree-Fock basis sets for the 5d transition
metals, especially Pt and Au. If you know of any ftp site containing these
type of basis sets or have references for relativistic HF basis sets, please
e-mail me at the address below.
Thank you.
Leslie
perkins@iastate.edu
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Leslie S. Perkins Department of Chemistry - Ames Laboratory
402 Wilhelm Hall e-mail : perkins@tc4.fi.ameslab.gov
Iowa State Univ. voice : (515) 294-9925
Ames, Iowa 50011 fax : (515) 294-5204
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
From chemistry-request@ccl.net Fri Jul 17 14:56:14 1992
Date: Fri, 17 Jul 92 13:21 EDT
From: <SML108@PSUVM.PSU.EDU>
Subject: Amber residue vs. atom based cutoffs
To: chemistry@ccl.net
Status: R
Hi, I have a question. AMBER is billed as a residue based force field.
On this account, it is claimed, it uses a residue based cutoff for
non-bond interactions. Has anyone ever tested what happens when an atom
based cutoff is used? Does it actually make a difference? One can
think of reasons why it would and reasons why it might not..
Scott
From chemistry-request@ccl.net Fri Jul 17 19:50:28 1992
Date: Fri, 17 Jul 1992 11:32 MST
From: YAMAMURA@CGF.chem.Arizona.edu
Subject: Interaction Energy and Hydrophobicity
To: chemistry@ccl.net
Status: R
Dear Fellow Netters,
Does anyone know of computational models for calculating interaction
energies between the planar surface of a solid of a known crystal structure
and the surface of an adsorbed protein of known crystal structure? It is
especially desirable for the model to include hydrophobic interactions.
All information received will be summarized to the net. Any information
about references, programs, etc would be very much appreciated.
Thank you.
Susan Yamamura
yamamura@cgf.chem.arizona.edu