From chemistry-request@ccl.net Tue Dec  7 10:22:23 2004
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Date: Tue, 07 Dec 2004 09:40:17 -0600
From: Pijush Ghosh <pijush.ghosh~at~ndsu.nodak.edu>
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Subject: CCL:  Computation Resource Requirement.
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CCL Users,
       being new to the field of computational quantum mechanics, i have 
a basic question on the requirement of the resources for this type of 
computation.  Can anybody  cite any reference where i can get some 
relation between number of processors and time required  with that of 
number of atoms in a system , basis set used, etc.
     
In my system of Hydroxyapatite- polymer I have the following details:

atom                 number

Calcium              20
Phosphorous      12
Oxygen              54
Hydrogen           10
Carbon                 3


Basis set -            6-31+G**
Method -              HF (Hartree Fock)


can somebody  give idea on  processor-hour required. All my simulations 
are run on NCSA machines.


All suggesions and information appreciated in advance.


Pijush Ghosh.
NDSU.



From chemistry-request@ccl.net Mon Dec  6 11:37:28 2004
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Date: Tue, 7 Dec 2004 00:52:28 +0800 (CST)
From: Jinsong Zhao <zh_jinsong/at/yahoo.com.cn>
Subject: CCL: DOCK: prepare a mol2 file for receptor  
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Dear all,

Preparation of a mol2 file for receptor seems a crucial step in
DOCKing. I find it's very difficult even I can use SYBYL.

Firstly, I am not sure that histidine residues should be named to HIS,
HIP, HID or HIE. And cysteine residues is also the problem. Are there
any conventions?

Secondly, how to avoid the non-integer charges for certain residue?
Does it mean that if a residue contain missing atom, then it will
charge a non-integer charges?

Any suggestions will be really appreciated! Thanks in advance!

Best wishes,
Jinsong


=====
(Mr.) Jinsong Zhao
Ph.D. Candidate
School of the Environment
Nanjing University
No.22 Hankou Road, Najing 210093
P.R. China
E-mail: zh_jinsong/at/yahoo.com.cn

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From chemistry-request@ccl.net Mon Dec  6 11:16:39 2004
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Date: Mon, 6 Dec 2004 08:31:44 -0800 (PST)
From: IEJMD <iejmd$at$yahoo.com>
Subject: IECMD 2004 - Conference Program for December 6-10
To: CCL <chemistry$at$ccl.net>
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Internet Electronic Conference of Molecular Design 2004
IECMD 2004, November 29 - December 12
http://www.biochempress.com

All accepted papers are posted on the Web and can be downloaded
as PDF files from http://www.biochempress.com
The complete Conference program is included below.

The discussions of the IECMD 2004 papers will take place on the Web,
using the Yahoo! group iecmd2004, http://groups.yahoo.com/group/iecmd2004

Please visit the IECMD 2004 discussion site at
http://groups.yahoo.com/group/iecmd2004 to sign-up and
send comments to the group.
Subscribe: 	iecmd2004-subscribe$at$yahoogroups.com

Best regards,
IECMD 2004 Organizers
----------------------------------
IECMD 2004, Day 6, December 6

1. IECMD 2004, paper 36
Numerical Evaluation of Two-Center Overlap Integrals Over Slater-Type
 Orbitals and Convergence Properties
Hassan Safouhi and Ahmed Bouferguene

2. IECMD 2004, paper 22
The nano-science of C60 molecule
Elena F. Sheka

3. IECMD 2004, paper 25
New Application Design for a 3D Hydropathic Map-Based Search for
 Potential Water Molecules Bridging between Protein and Ligand
Glen E. Kellogg , Micaela Fornabaio , Deliang L. Chen , and Donald J. Abraham

4. IECMD 2004, paper 16
Property-Based Design Methodology III: Identifying Creative Substituents
R. DeWitte , E. Kolovanov , and F. Gorohov

5. IECMD 2004, paper 42
General and independent approaches to predict HERG affinity values
Elena Fioravanzo , Nicola Cazzolla , Lucia Durando , Cristina Ferrari ,
 Massimo Mabilia , Rosella Ombrato , and Marco Daniele Parenti 

6. IECMD 2004, paper 50
The Infrared and Raman Spectroscopic Signals of HF, HCl, HBr and HI
Martin Grayson 
-----------------------------------------------------------------------
IECMD 2004, Day 7, December 7

1. IECMD 2004, paper 45
Reduced Protein Model as a Tool in the Homology Modeling
Andrzej Szymoszek and Martin Zacharias

2. IECMD 2004, paper 38
On the Charge Transfer Between a Toxin and a Biosystem
Utpal Sarkar , Ramakrishnan Parthasarathi , Venkatesan Subramanian ,
 and Pratim Kumar Chattaraj

3. IECMD 2004, paper 24
Thermochemistry of Organic and Heteroorganic Species. Part XIV.
 Application of IR Spectra of the Unsaturated Aliphatic Molecules
 for Thermochemistry of Vinylic and Allylic Free Radicals
D. A. Ponomarev and V. V. Takhistov

4. IECMD 2004, paper 17
Property-Based Design Methodology IV: Heterocycle Replacement
R. DeWitte , E. Kolovanov , and F. Gorohov

5. IECMD 2004, paper 3
Conformations of 2-Phenyl-3-Pyridylpropenoic Acid (a-Phenyl Pyridylcinnamic
 Acid) Dimers   A Computational Study
Istvan Palinks 
-----------------------------------------------------------------------
IECMD 2004, Day 8, December 8

1. IECMD 2004, paper 39
Adsorption Models of Bipyrazine on Silver Colloidal Nanoparticles:
 a Computational Study
B. Pergolese , M. Muniz-Miranda , and A. Bigotto

2. IECMD 2004, paper 11
A Theory of the Colossal Van-der-Waals Binding in Soft and Hard Condensed
Matter
Mladen Georgiev , Alexander Gochev , and Jai Singh

3. IECMD 2004, paper 9
A Predictive Model for Blood-Brain Barrier Penetration
Xuchun Fu , Zhifang Song , and Wenquan Liang

4. IECMD 2004, paper 8
Modeling Human Neurokinin-1 Receptor Structure using the Crystal
 Structure of Bovine Rhodopsin
Santosh A. Khedkar , Alpeshkumar K. Malde , and Evans C. Coutinho 

5. IECMD 2004, paper 49
A Multivariate Study on the Inhibition of the Xanthine Oxidase
 by Phenylpyrazole Compounds
S. L. da Silva , S. Marangoni , K. C. Weber , P. Homem-de-Mello ,
 K. M. Honsrio , and Alberico Borges Ferreira da Silva 
-----------------------------------------------------------------------
IECMD 2004, Day 9, December 9

1. IECMD 2004, paper 37
Use of Lanczos Tau Method to Derive Polynomial Approximate from the Addition
 Theorem of Slater Type Orbitals
Ahmed Bouferguene and Hassan Safouhi

2. IECMD 2004, paper 7
Study of the Glass Transition Temperatures of Stereoregular PMMAs
 Using Different Force Fields
Armand Soldera and Noureddine Metatla

3. IECMD 2004, paper 18
Numerical characterization of RNA secondary structure
Jiaquan Zhan , Bo Liao , and Yusen Zhang

4. IECMD 2004, paper 31
Peptide Potential Energy Surfaces and Protein Folding
Francisco Torrens 

5. IECMD 2004, paper 46
Molecular Structure and Reactive Sites of Substituted
 Di-(4-hydroxycoumarin)s Derived from DFT Calculations
Natasha Trendafilova and Tzvetan Mihaylov

6. IECMD 2004, paper 47
Renormalized Protein Folding of Cancerogenesis Proteins
Vincenzo Villani , Ciro Leonardo Pierri , and Alfonso Cascone 
-----------------------------------------------------------------------
IECMD 2004, Day 10, December 10

1. IECMD 2004, paper 4
pH-Dependent Complexation of Methacryloyloxydecyl Dihydrogen Phosphate
 (MDP) with Dipalmitoylphosphatidylcholine (DPPC) Liposomes:
 DSC and NMR Measurements
Seiichiro Fujisawa , Mariko Ishihara , and Yoshinori Kadoma

2. IECMD 2004, paper 12
Molecular Volume and Density Models for Alkanes and Monoderivatives of
Hydrocarbon
Chenzhong Cao and Shuo Gao

3. IECMD 2004, paper 27
Qspr Evaluation of Thermodynamic Properties of Acyclic and Aromatic Compounds
Pablo R. Duchowicz , Eduardo A. Castro , and Alexei N. Pankratov

4. IECMD 2004, paper 13
Finding Protein Coding Genes in the Yeast Genome Based on the Characteristic
Sequences
Ping-an He , Chun Li , and Jun Wang 

5. IECMD 2004, paper 48
1,5-N,N'-Disubstituted-2-(Substituted Benzenesulphonyl)-Glutamamide
 Analogues as Anticancer agents   part 3: Synthesis, Biological
 Screening and QSAR Study
Shovanlal Gayen , Bikash Debnath , Soma Samanta , Balaram Ghosh ,
 Anindya Basu , and Tarun Jha


		
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The all-new My Yahoo! - Get yours free! 
http://my.yahoo.com 
 



From chemistry-request@ccl.net Mon Dec  6 11:09:02 2004
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Date: Mon, 6 Dec 2004 16:24:06 +0000 (GMT)
From: =?iso-8859-1?q?i=FFfffff1igo=20garcia=20yoldi?= <garciayoldi^at^yahoo.co.uk>
Subject: GAUSSIAN 03. DFT models
To: chemistry^at^ccl.net
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Dear list.

At Gaussian 03 the DFT methods are defined by six
parameters that you can modify with the iop(5/45),
iop(5/46) and iop(5/47). In a DFT calculation their
values are 1.0, 0.2, 0.72, 0.8, 0.81 and 0.1.

Does anybody knows the values in PBEPBE and PW91PW91
calculation? I try to find them in the vectors ScaHFX
and ScaDFX but it does not appear.

Thanks a lot



		
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From chemistry-request@ccl.net Tue Dec  7 06:46:34 2004
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To: <CHEMISTRY)at(ccl.net>
Subject: CCL: Latest PC GAMESS version 6.5 final release candidate preview/test program
Date: Tue, 7 Dec 2004 15:01:09 +0300
Organization: MSU
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Dear PC GAMESS users!

After 9 months of constant development, we are almost done with the new PC GAMESS version 6.5.
Namely, the final release candidate (RC9) is available for your testing upon request. The only condition to 
participate in the test/preview program is that you must be one of the registered users of the PC GAMESS 
versions 6.3 or 6.4. If you like to try the new version, please send email directly to me (not to this list!) 
and you'll be provided by the necessary instructions. 

Best regards,
Alex Granovsky






From chemistry-request@ccl.net Mon Dec  6 11:52:29 2004
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From: "ELAMBALASSERY, JAYASREE" <jayaeg..at..berkeley.edu>
Subject: NWchem: optimization problem
To: chemistry..at..ccl.net
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Dear all,

I tried an optimization job of simple molecule (allyl fluoride) using NWChem 4.5. It reproduced 
the energy and geometry which I got from Gaussian calculations. I ran the above job in DATASTAR at 
San Diego (SDSC IBM DataStar Power4). Now I tried running another job but it converges to a point 
far away from the minimum and gives me more than 70 imaginary frequency. When I tried with tight 
convergence, it converged to another point with 28 imaginary frequencies. The input is attached 
below. Can you pls tell me where I went wrong? Gaussian optimized geometry is taken as the input 
in this case. Thank you very much
Jayasree

******************input***********************
scratch_dir /scratch

permanent_dir .

restart 14cot

title "14cot"

geometry units angstroms autosym
  C 1.22985 -1.06641 0.68744
  H 1.69955 -1.7696 1.37073
  C 1.37469 0.24475 0.93719
  H 1.96198 0.55484 1.79803
  C 0.55145 -1.65633 -0.46926
  C -0.75312 -1.40745 -0.71867
  H -1.25431 -1.89237 -1.5518
  C 0.85554 1.31703 0.12136
  C -0.44029 1.52588 -0.16094
  H -0.69626 2.39261 -0.7653
  C -1.57038 0.73206 0.32788
  C -1.66695 -0.58888 0.05984
  H -2.53628 -1.15259 0.38683
  H 1.59529 2.02231 -0.2494
  C 1.42464 -2.59451 -1.34568
  C -2.63907 1.52066 1.1321
  C 0.73672 -3.02544 -2.66467
  H 1.40752 -3.63935 -3.27799
  H 0.44955 -2.15745 -3.26953
  H -0.15884 -3.62886 -2.47703
  C -3.39844 2.48878 0.19959
  H -2.74376 3.26394 -0.21267
  H -4.20243 3.00506 0.73744
  H -3.85363 1.95249 -0.64122
  C 1.76236 -3.88525 -0.56889
  H 2.32203 -4.58846 -1.19697
  H 0.8515 -4.39417 -0.23257
  H 2.38021 -3.68676 0.31332
  C 2.74101 -1.8895 -1.74832
  H 3.33964 -2.52087 -2.41564
  H 3.37038 -1.66322 -0.88039
  H 2.54052 -0.94848 -2.27392
  C -3.69901 0.61424 1.8056
  H -3.23345 -0.11726 2.47634
  H -4.2995 0.07297 1.06546
  H -4.39935 1.20555 2.40801
  C -1.97253 2.33284 2.26704
  H -1.29743 3.10466 1.88085
  H -1.39406 1.68103 2.93223
  H -2.72321 2.84787 2.8782
end

basis
  C Library 6-31++G*
  H Library 6-31++G*
end

scf
  rhf
  singlet
end

driver
  maxiter 200
  tight
end

task scf optimize

task scf freq

******
Elambalassery G. Jayasree
Prof Streitwieser group
University of California
Berkeley-94720
Ph (510) 642-0796.


From chemistry-request@ccl.net Mon Dec  6 19:37:59 2004
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Subject: nanomathematics
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Hi, all,

Would anyone give a description about the concept "nanomathematics"?


Thanks in advance.

Chungen


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I've never seen the term before, but logically it should refer to arithmetic in which all numbers are rounded off to the nearest billionth.  :-)

--David Shobe, Ph.D., M.L.S.
S|d-Chemie, Inc.
phone (502) 634-7409
fax (502) 634-7724

Don't bother flaming me: I'm behind a firewall.


-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request{at}ccl.net]On
Behalf Of Chungen Liu
Sent: Monday, December 06, 2004 7:44 PM
To: chemistry{at}ccl.net
Subject: CCL:nanomathematics


Hi, all,

Would anyone give a description about the concept "nanomathematics"?


Thanks in advance.

Chungen


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