From chpajt@bath.ac.uk  Wed Jul 17 04:14:35 1996
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Date: Wed, 17 Jul 1996 08:53:58 +0100 (BST)
From: A J Turner <chpajt@bath.ac.uk>
To: CHEMISTRY@www.ccl.net
Subject: G77/charmm
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Hi!

Does anyone 

A: know where to get hold of G77 (gnu f77)

B: Have any experiance at building charmm from G77 (it seems to have a
compiler flag of it).

Thanks in advance

Alex

 -------------------------------------------------------------------
|Alexander J Turner         |A.J.Turner@bath.ac.uk                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
 ------------------------------------------------------------------- 



From chpajt@bath.ac.uk  Wed Jul 17 04:28:11 1996
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Date: Wed, 17 Jul 1996 08:56:27 +0100 (BST)
From: A J Turner <chpajt@bath.ac.uk>
To: CHEMISTRY@www.ccl.net
Subject: M: FORCE and EF
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Hi!

I noticed a request for why EF and FORCE are incompatable in MOPAC.  Sorry
if this has already been answered - 

They are incompatable as FORCE automatically invokes BFGS to get the
gradient down to an acceptable level (even if it is already OK - it still
thinks that it will use BFGS).

The only simple answer is the use an EF .arc file to fire up a FORCE job.

Cheers

Alex

 -------------------------------------------------------------------
|Alexander J Turner         |A.J.Turner@bath.ac.uk                  |
|Post Graduate              |http://www.bath.ac.uk/~chpajt/home.html|
|School of Chemistry        |+144 1225 8262826 ext 5137             |
|University of Bath         |                                       |
|Bath, Avon, U.K.           |Field: QM/MM modeling                  |
 ------------------------------------------------------------------- 



From rochus@felix.anorg.chemie.tu-muenchen.de  Wed Jul 17 05:14:35 1996
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From: "Rochus Schmid" <rochus@felix.anorg.chemie.tu-muenchen.de>
Message-Id: <9607171105.ZM13721@felix>
Date: Wed, 17 Jul 1996 11:05:52 -0600
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To: chemistry@www.ccl.net
Subject: performance of PPro
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Dear Netters,

I know that this issue appears quite often on this list. I checked a number of
webpages concerning benchmarks but couldn't find the infos. Please forgive me.

We want to buy a new workstation for running e.g. Gaussian or related
QM-packages. Because of beeing confident with SGI INDY's we checked them first.
However, we found that the Pentium Pro 200 MHz has HIGHER SPECfp95 values than
the R5000 150 MHz and is MUCH cheaper.

But I guess that SPECfp95 is not the whole story.
Does anyone of you have experience about the performance in "real applications"
of PPro Systems running LINUX (e.g. in comparison with R5000 SC 150MHz INDY
running IRIX).

Since I can buy two PPro for one INDY this is a real problem for me.
Thank you very much in advance. I will summarize.

Rochus

-- 

********************************************************************************
Rochus Schmid
Technische Universitaet Muenchen	Tel. 	++49 89 2891 3140
Lehrstuhl f. Anorganische Chemie 1	Fax. 	++49 89 2891 3088
Prof. W. A. Herrmann			E-mail:	
Lichtenbergstrasse 4			rochus@felix.anorg.chemie.tu-muenchen.de
85747 Garching
********************************************************************************

From chrirena@techunix.technion.ac.il  Wed Jul 17 07:14:43 1996
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Date: Wed, 17 Jul 1996 13:14:33 +0300 (IDT)
From: Irena Efremenko <chrirena@techunix.technion.ac.il>
To: CHEMISTRY@www.ccl.net
Subject: Parametrization for highly charged clusters?
In-Reply-To: <Pine.3.05.9604241121.A55866-e100000@che.udel.edu>
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Dear CCL'ers,
 
I am trying to do simulations of clusters on the strongly biased
surface (about 100-200 V) by ASED MO calculations (total energy equal sum
of Extended Huckel attractive and pair-wize atom-atom repulsive energies).
In the framework of this method there are 3 connected parameters depending
of bias: charge of cluster, ionization potentials and Slater orbital
exponents. So, my questions are:
1) Is anybody aware of such parameters dependence of bias and to one
another?
2) How can I estimate the cluster stability? Is it possible to get bounded
surface cluster with charge +6 or -6 per a few atoms?
3) Any references to the experimental or other calculation data which can
help to do a reasonable model and some not very expansive ways to
parametrize it.

Thank you in advance,

Of course I'll summarize the responses if there is an interest.

Irena

------------------------------------------------------------------------------- 
Irena Efremenko, PhD

Department of Chemistry
Technion, Israel Institute of Technology    chrirena@technion.techunix.ac.il
-------------------------------------------------------------------------------


From wieland@btm2d1.mat.uni-bayreuth.de  Wed Jul 17 08:14:36 1996
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To: chemistry@www.ccl.net, thomas_g@btm2xi.mat.uni-bayreuth.de
Subject: Retention indices in GC
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Dear Colleagues,

a co-worker in our institute is looking for a method to calculate retention
indices of compounds for use in gas chromatography.

All we have is a paper by Peng et. al. (J. Chromat., 436 (1988), 137)
where a rather obscure methods is described.

If anybody knows about a more modern and more systematic approach
in literature, we would be glad to hear about it. Hints to programs
for such calculations would be highly appreciated, too.

I will summarize to the net if there is enough interest.

Best regards,
Thomas Wieland


From owner-chemistry@ccl.net  Wed Jul 17 09:14:36 1996
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From: gdanitz@hrz.uni-kassel.de (Robert Gdanitz)
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Subject: Full-CI calculation of Be wanted!
To: chemistry@ccl.net (Computational Chemistry List)
Date: Wed, 17 Jul 1996 14:52:30 +0200 (MES)
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Dear Colleagues,
I would appreciate it, if anybody could inform me about a recent full-CI calcu-
lation on the ground state of Beryllium atom with all 4 electrons correlated, 
preferably in a rather large gaussian basis set. 
This information would considerably help me to calibrate my method.
Thank you in advance!
Robert Gdanitz
-- 
+-----+  Robert J. Gdanitz                      email: gdanitz@hrz.uni-kassel.de
| GhK |  Gesamthochschule Kassel                Tel.: +(49) 561-804-4556
|     |  Fachbereich 18 (Physik)                Fax:  +(49) 561-804-4006
+-----+  D-34109 Kassel, Germany

From tp@elptrs7.rug.ac.be  Wed Jul 17 10:14:37 1996
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Date: Wed, 17 Jul 1996 15:28:33 +0200 (DFT)
From: "Park, Tae-Yun" <tp@elptrs7.rug.ac.be>
To: Computational Chemistry List <chemistry@www.ccl.net>
Subject: Help!: IRC by mopac
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  This message is in MIME format.  The first part should be readable text,
  while the remaining parts are likely unreadable without MIME-aware tools.
  Send mail to mime@docserver.cac.washington.edu for more info.

---1648267236-2078917053-837506593=:20692
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Dear all,

*************************************************************
I'm sending this message one more time, since my previous
e-mail was not responded in more than 1 day.  Please execuse
me if you receive this message twice.
*************************************************************

I'm searching the structure of the transition state with 
mopac for the reaction type,

    olefin + carbenium ion ---> (TS?) ---> carbenium ion  (1)

My previous try for the reaction,


   H              H     H                       H H H
   |               \   /                        | | |
 H-C(+)       +     C=C     ---->(TS?)---->   H-C-C-C(+) 
   |               /   \                        | | |
   H              H     H                       H H H

 gas-phase                                     gas-phase
   methyl         ethylene                   primary propyl
carbenium ion                                 carbenium ion

has been found that there is no transition state, thanks to 
great help from many CCLers, since the gas-phase methyl 
carbenium ion is too unstable.

Actually I'm dealing with more than 100 reactions which have
the reaction type written in (1).  Therefore, I tried with 
other reaction, which contains more stable species, i.e.,

                    H  
                    |                      H
    H         H   H-C-H                   HCH H H H
  H | H        \   /                     H |  | | |  
 HC-C-CH   +    C=C    ---->(TS?)---->  HC-C--C-C-C-H
  H + H        /   \                     H |  | + |
              H     H                      H  H   H
secondary
  propyl      propene                   secondary 2-M
carbenium                              pentyle carbenium
          

Searching the TS in this reaction, I followed the suggestion
by many CCLers, i.e., try to get the TS structure by the 
following steps instead of using SADDLE calculation:

1. Try the reacion path calculation in mopac and save the 
   structure that contains the highest energy level.

2. Refine the structure at highest energy level with key 
   word, NLLSQ, or SIGMA, or TS.

3. FORCE calculation with the refined structure to check 
   if there is one and only one negative frequecy value.

4. Do IRC(=1 and -1) calculation to check if the refined 
   TS gives the reactants and product.

My result is that until step 3, everything seems OK.  Refinning
the TS by NLLSQ/SIGMA/TS gives no significant change of the TS
that obtained from step 1, probably because I used the key word
PRECISE in step 1.  The FORCE calculation showed that the refined
structure contains only one frequency values.

My problem is in the last step.  When I do the IRC calculation
and try to look at the result structure with "molden" software,
it gives exactly same as the structure of TS I input.

I wonder if (i) my TS is not correct, or (ii) the IRC calculation
doesn't give the molecular structure result from the calculation
so that molden only edit the structure I input.  In the latter
case, however, I don't know how to edit the molecluar structure
generated by IRC calculation.

Could anyone PLEASE help me how to confirm my TS structure by IRC?

I enclosed the input/result file at the end of this message.

Thank you very much in advance.


				Sincerely,

				     Park, TAE-YUN    
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
State University of Ghent
Laboratorium voor Petrochemische Techniek
Krijgslaan 281, Blok S5  
9000 Gent, Belgium	  
TEL:+(32)-0(9)-264-4527
FAX:+(32)-0(9)-264-4999
e-mail: tp@elptrs7.rug.ac.be
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=


Data Files for the 4 steps.  Please note that the result file of 
step 1 is the input file for step 2... etc.

----------------------------------------------------------------
Step 1 input file:

CHARGE=1 PRECISE GRAPH DENSITY
r3_s-o3.dat

C    0.000000  0    0.000000  0    0.000000  0    0   0   0
C    1.437805  1    0.000000  0    0.000000  0    1   0   0
C    4.501968 -1   96.018692  1    0.000000  0    1   2   0
C    1.331116  1   87.080215  1 -155.227356  1    3   1   2
C    1.476334  1  124.262665  1 -135.173477  1    4   3   1
C    1.437424  1  123.306213  1  133.821869  1    1   2   3
H    1.135651  1  110.106583  1  123.092896  1    2   1   6
H    1.120895  1  114.528610  1    0.000000  1    2   1   6
H    1.135742  1  110.066360  1 -123.042191  1    2   1   6
H    1.115219  1  118.018661  1  -56.365555  1    1   2   7
H    1.097427  1  122.281586  1 -179.999634  1    3   4   5
H    1.097809  1  122.792145  1    0.000000  1    3   4   5
H    1.103470  1  120.865265  1    0.000000  1    4   3  11
H    1.118958  1  110.075104  1 -120.477097  1    5   4   3
H    1.119080  1  110.076859  1  120.510315  1    5   4   3
H    1.117584  1  111.867340  1    0.000000  1    5   4   3
H    1.121948  1  113.719040  1 -179.999634  1    6   1   2
H    1.134903  1  110.648621  1   57.360474  1    6   1   2
H    1.134933  1  110.636383  1  -57.367462  1    6   1   2
0    0.000000  0    0.000000  0    0.000000  0    0   0   0
4.0 3.5 3.0 2.8 2.6 2.5 2.4 2.3 2.2 2.1 2.0 1.9 1.8 1.7 1.6 1.55

----------------------------------------------------------------
Step 2 input file(for NLLSQ):

NLLSQ CHARGE=1 PRECISE DENSITY GRAPH
Optimizing ts

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.493971 1     .000000 0     .000000 0       1    0    0
 C    2.400000 1   99.829562 1     .000000 0       1    2    0
 C    1.366739 1  107.774987 1 -156.603212 1       3    1    2
 C    1.495494 1  127.295132 1  -95.474920 1       4    3    1
 C    1.493103 1  122.565420 1  111.465448 1       1    2    3
 H    1.108922 1  112.541937 1  169.169618 1       2    1    6
 H    1.109391 1  113.333661 1   45.130877 1       2    1    6
 H    1.118316 1  107.399773 1  -73.220364 1       2    1    6
 H    1.098555 1  116.705711 1  -32.527608 1       1    2    7
 H    1.092716 1  119.490590 1  165.857707 1       3    4    5
 H    1.091757 1  122.354434 1    9.374023 1       3    4    5
 H    1.098702 1  118.584661 1  -13.736600 1       4    3   11
 H    1.111796 1  109.120250 1 -115.208112 1       5    4    3
 H    1.110446 1  110.429073 1  126.570168 1       5    4    3
 H    1.107787 1  113.319142 1    4.958871 1       5    4    3
 H    1.108134 1  112.416348 1 -172.721816 1       6    1    2
 H    1.118042 1  107.755456 1   69.492728 1       6    1    2
 H    1.109678 1  113.288218 1  -48.800221 1       6    1    2

----------------------------------------------------------------
Step 3 input file (for NLLSQ):

FORCE CHARGE=1 DENSITY GRAPH ISOTOPE
TS checking by FORCE calculation

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.494700 1     .000000 0     .000000 0       1    0    0
 C    1.493679 1  122.365784 1     .000000 0       2    1    0
 C    2.380560 1  102.504395 1  110.467232 1       2    3    1
 C    1.368080 1  107.971291 1   74.388344 1       4    2    3
 C    1.495277 1  127.264130 1  -95.821228 1       5    4    2
 H    1.108898 1  112.496826 1  169.901352 1       1    2    3
 H    1.109529 1  113.296120 1   46.004711 1       1    2    3
 H    1.117890 1  107.496994 1  -72.487534 1       1    2    3
 H    1.098734 1   86.146576 1  -42.602459 1       2    4    5
 H    1.092931 1  119.365471 1  165.091675 1       4    5    6
 H    1.092000 1  122.211273 1    9.421019 1       4    5    6
 H    1.098602 1  118.611084 1   84.593826 1       5    4    2
 H    1.111888 1  109.074448 1 -114.666496 1       6    5    4
 H    1.110686 1  110.417656 1  127.198174 1       6    5    4
 H    1.107639 1  113.346970 1    5.549870 1       6    5    4
 H    1.108230 1  112.441048 1 -172.787689 1       3    2    1
 H    1.117836 1  107.759140 1   69.464531 1       3    2    1
 H    1.109580 1  113.282127 1  -48.948452 1       3    2    1

-----------------------------------------------------------------
Step 4 input file (for NLLSQ and for backward reaction, i.e, IRC=-1)
       This step is restarted immediately after the step 3.


IRC=-1 RESTART CHARGE=1 DENSITY GRAPH ISOTOPE
TS checking by IRC calculation

 C     .000000 0     .000000 0     .000000 0       0    0    0
 C    1.494700 1     .000000 0     .000000 0       1    0    0
 C    1.493679 1  122.365784 1     .000000 0       2    1    0
 C    2.380560 1  102.504395 1  110.467232 1       2    3    1
 C    1.368080 1  107.971291 1   74.388344 1       4    2    3
 C    1.495277 1  127.264130 1  -95.821228 1       5    4    2
 H    1.108898 1  112.496826 1  169.901352 1       1    2    3
 H    1.109529 1  113.296120 1   46.004711 1       1    2    3
 H    1.117890 1  107.496994 1  -72.487534 1       1    2    3
 H    1.098734 1   86.146576 1  -42.602459 1       2    4    5
 H    1.092931 1  119.365471 1  165.091675 1       4    5    6
 H    1.092000 1  122.211273 1    9.421019 1       4    5    6
 H    1.098602 1  118.611084 1   84.593826 1       5    4    2
 H    1.111888 1  109.074448 1 -114.666496 1       6    5    4
 H    1.110686 1  110.417656 1  127.198174 1       6    5    4
 H    1.107639 1  113.346970 1    5.549870 1       6    5    4
 H    1.108230 1  112.441048 1 -172.787689 1       3    2    1
 H    1.117836 1  107.759140 1   69.464531 1       3    2    1
 H    1.109580 1  113.282127 1  -48.948452 1       3    2    1

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

---1648267236-2078917053-837506593=:20692--

From medven@olimp.irb.hr  Wed Jul 17 11:14:38 1996
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	by www.ccl.net (8.7.5/950822.1) id KAA16041; Wed, 17 Jul 1996 10:41:34 -0400 (EDT)
From: <medven@olimp.irb.hr>
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To: CHEMISTRY@www.ccl.net
CC: medven@olimp.irb.hr
Message-ID: <009A5787.41D6B2AC.3@olimp.irb.hr>
Subject: summary on QM calculations on hydrogen bonds


A week ago, I posted a question regarding QM calculations on hydrogen bonded structures comprising nucleic acic bases and other nitrogen containing aromatics. Here is a short summary of responses. Thanx to all who responded.
--------------------
From Vladislav VASILYEV
Some nitrogen containing aromatics (semiempirical and comparison with ab
initio) you can find in:
 V.V. Vasilyev, A.A. Bliznyuk, and A.A. Voityuk, A Combined Quantum
   Chemical/Molecular Mechanical Study of Hydrogen-Bonded Systems.//
   Int.J.Quantum.Chem., 44(1992), 897-930.
--------------------
From Irene Newhouse
There are lots of references;  some work was done by Jerzy Leszczynski a few
years back.  I think it came out in one of the ACS [American Chemical Society]
publications, which you may have access to.  It should give references you
can then go hunt down.
--------------------
From Bill Ross
Much ab initio work on nucleic acids has been done by
J. Sponer, P. Hobza, J. Florian and their collaborators, e.g.
 Bifurcated H Bonds in DNA Xtl Structs. An ab Initio Quantum Chem Study
 Sponer & Hobza JACS 116, 709-714 (1994)
 Ab init .. G-C base pair conformers in gas phase & polar solvents
 Florian, Leszczynski, Scheiner, Molec. Phys. 84:3, 469-480 (1995)
--------------------
From Ryszard Czerminski
 5. R. Czermi\o"n\'"ski, K. Kuczera, H. Rostkowska, M. Nowak and K.
Szczepaniak
"Autoassociates and Tautomerism of 2-oxo-5-halogeno-pyrimidines :
Theoretical and Experimental Investigations"
J. Mol. Struct. 140, 235 (1986)
 6. R. Czermi\o"n\'"ski
"Intermolecular Interactions : Reliability of Results Obtained for
Small Hydrogen Bonded Dimers by Claveries Method"
Int. J. Quant. Chem. 31, 649 (1987)
 7. R. Czermi\o"n\'"ski  "Reparametrization
of Claverie's Method for Intermolecular Energy Calculation"
J. Mol. Struct. 170, 245 (1988)
 9. W.B. Person, K. Szczepaniak, M. Szczesniak, J.S. Kwiatkowski, L.
Hernandez and R. Czermi\o"n\'"ski
"Tautomerism of Nucleic Acid Bases and the Effect of Molecular
Interactions on Tautomeric Equilibria"
J. Mol. Struct. 194, 239 (1989)
 10. R. Czermi\o"n\'"ski, J.S. Kwiatkowski, W.B. Person and K.
Szczepaniak -
"Quantum-Mechanical Studies of the Structures of Cytosine Dimers
and Guanine-Cytosine Pairs"
J. Mol. Struct. 198, 297 (1989)
 15. R. Czermi\o"n\'"ski, K. Szczepaniak, W.B. Person, J.S. Kwiatkowski
"Intermolecular Interactions and Tautomerism of Nucleic Acid Bases
and their Analogues"  J. Mol. Struct. 237, 151 (1990)
-----------------------
Enclosed is my list of other references:
1) Z. Dega-Szafran, M. Gdaniec, M. Grundwald-Wyspianska, Z. Kosturkiewicz, J Koput, P. Krzyzanowski, M. Szafran (on X-ray, FT-IR and PM3 studies of H-bonded complexes of some pyridines), J. Mol. Struct. 270 (1992) 99.
2) S.G. Stepanian, G.G. Sheina, E.D. Radchenko (MNDO/M study of pyrimidine bases), Yu.P. Blagoi, J. Mol. Struct. 270 (1992) 459.
3) A. Destexhe, J. Smets, L. Adamowicz, G. Maes (ab initio studies of pyridine and pyrimidine complexes with water), J.Phys. Chem. 98 (1994) 1506.
4) J. Smets, L. Adamowicz, G. Maes (ab initio studies of 4-aminopyridine and 4-aminopyrimidine complexes with water), J.Phys. Chem. 99 (1995) 6387.

                           Cheers,
                                                     Zeljka


**********************************************************************
M.Sc. Zeljka Medven                           Area code: 385-1
Department of Chemistry                       Phone:     456-1089
Rugjer Boskovic Institute                     Fax:       272-648
POB 1016, HR-10001 Zagreb, Croatia            e-mail:    medven@olimp.irb.hr
**********************************************************************

From d3g359@fido.pnl.gov  Wed Jul 17 13:14:39 1996
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Date: Wed, 17 Jul 1996 10:02:50 -0700
From: d3g359@fido.pnl.gov (John Nicholas)
Subject: SCI-PCM Model in G94
To: CHEMISTRY@www.ccl.net
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I have been having problems getting geometries (and in some cases SCF's)
to converge when using the scrf=scipcm option in G94. The higher
the dielectric constant, the more problem there seems to be. Does
anyone have any suggestions on how this problem might be cured? I
have already started with prior hessians and the molecules are simple,
so the problem seems to be the inclusion of solvent effects.

Thanks in advance, John


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