From chemistry-request@ccl.net Tue Apr 27 02:12:36 2004
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Date: Thu, 27 Nov 2003 09:13:51 +0100
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From: Jesus Rodriguez-Otero <qftjesus:at:usc.es>
Subject: CCL: Pd-ethylene cluster with G98
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Hi netters,

I am comparing the performance of HF, DFT/B3LYP anda MP2 with Gaussian98 in 
a simple
calculation of a cluster formed by two Pd atoms and ethylene. To my 
surprise, b3lyp is
much slower than HF or MP2; cpu times are

hf: 	3 min. 21 s.
b3lyp:	1 h. 5 min.
mp2:	8 min. 28 s.

P-IV running LINUX

this is my input file:
------------------------------------------------------------------------------------
%chk=pd2etepa.chk
# hf/lanl2mb opt(z-matrix,maxcyc=60) scf(qc,maxcyc=500)

Title Card Required

0  1
  Pd
  Pd                 1        2.750872
  C                  1              B1    2              A1
  C                  3              B2    1              A2    2 
   D1
  H                  4              B3    3              A3    1 
   D2
  H                  3              B4    4              A4    5 
   D3
  H                  4              B5    3              A5    6 
   D4
  H                  3              B6    4              A6    7 
   D5

    B1             2.408742
    B2             1.354929
    B3             1.070182
    B4             1.070143
    B5             1.070035
    B6             1.069670
    A1            76.672064
    A2           107.368541
    A3           120.230124
    A4           119.863439
    A5           119.916731
    A6           120.275618
    D1             1.099106
    D2            90.171155
    D3             0.053786
    D4          -179.938316
    D5             0.015838
-------------------------------------------------------------------------------------------


Is this normal?
Can dft performance be improved?




                   \|/
               (  @ @  )
-------oOo-(_)-oOo------------------------------------------------------

Jeszs Rodrmguez-Otero
Departamento de Qummica Fmsica, Facultade de Qummica
Universidade de Santiago
15782 Santiago de Compostela, (Spain)
Phone: (+34)-981563100 ext 14436, Fax: (+34)-981595012
qftjesus:at:usc.es
http://web.usc.es/~qftjesus/index.html





From chemistry-request@ccl.net Tue Apr 27 02:31:52 2004
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Date: Tue, 27 Apr 2004 10:31:34 +3100 (Mideast/Riyadh)
From: "Adel Abbas Ali Elazhary    F# 69913 Sci. College" <azhary$at$ksu.edu.sa>
To: Ruth Tanner <rtanner$at$uoguelph.ca>
cc: CCL <chemistry$at$server.ccl.net>
Subject: Re: CCL:Problems with CCSD(T) jobs
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Dear Tanner

try "fulldirect" instead of "direct". I am not sure even that "maxdisk"
command really works!

Best regards,

Adel El-Azhary

On Sun, 25 Apr 2004, Ruth Tanner wrote:

>
> Despite having 143 GB of disk space and 1 GB of memory, I am unable to run
> the following job on my Windows machine for CF3CNO:
>
>  %mem=1000MB
>  %chk=cf3cno
>  Default route:  MaxDisk=48GB
>  ---------------------------------------------
>  #CCSD(T,conver=5,full)/6-311+G(2d) scfcyc=500
>  ---------------------------------------------
>
> and I get the following error:
>
>  **** Warning!!: The largest alpha MO coefficient is  0.93604856D+02
>
>  Estimate disk for full transformation   889596368 words.
>  Semi-Direct transformation.
>  ModeAB=           4 MOrb=             1 LenV=     130390762
>  LASXX=    128120103 LTotXX=   171968404 LenRXX=   214233243
>  LTotAB=    42264839 MaxLAS=   266972895 LenRXY=           0
>  NonZer=   298505045 LenScr=   449821184 LnRSAI=     2810241
>  LnScr1=     5240320 LExtra=           0 Total=    672104988
>  MaxDsk=           0 SrtSym=           T ITran=            5
>  File extend in NtrExt1 failed; probably out of disk space.
>
> Can anyone suggest a way I can get around this problem?  I should have
> enough disk space and memory, but I can't seem to get around this disk
> problem.
>
> Ruth
>
> ============================================================
> Ruth Tanner, B.Sc. M.Sc.                 rtanner$at$uoguelph.ca
> ------------------------------------------------------------
> ruth_tanner$at$yahoo.com			 rtanner$at$uwo.ca
> ============================================================
>
>
>
>
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From chemistry-request@ccl.net Tue Apr 27 09:46:37 2004
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Reply-To: jerome..at..scs.uiuc.edu
From: "Jerome Baudry" <jerome..at..scs.uiuc.edu>
To: chemistry..at..ccl.net
Subject: database agrochemicals/insecticides ?
Date: Tue, 27 Apr 2004 09:45:39 -0500
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Dear List,

I am looking for a database of agrochemicals compounds -in particular
insecticides- for use in V-HTS. Preferably in sdf format, but any electronic
format will do. Any quantity of information is fine, from just the structure
to catalog #, purity/price etc..

Any idea?

Thanks ,
Jerome

----------------------------------------------------------
Jerome Baudry, Ph.D.       Senior Research Scientist, VizLab Manager.
School of Chemical Sciences    University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801
 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120;    e-mail:
jerome..at..scs.uiuc.edu



From chemistry-request@ccl.net Tue Apr 27 13:33:50 2004
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Date: Tue, 27 Apr 2004 11:35:08 -0700 (PDT)
From: Liviu Mihail Mirica <liviu=at=stanford.edu>
To: chemistry=at=ccl.net
Subject: Frequency job in solvent
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Hi all,
I have a question regarding a Gaussian98 frequency job in a solvent. The
input section is given below:

#P gfinput iop(6/7=3)
#P RB3LYP/6-31G* scfcyc=400
#P guess=read geom=check scrf=(pcm,solvent=thf) freq

for some reason, the job seems to do the SP calculation in a solvent
over and over again. i let the job to run for a week, and all i got as
about 30 sp jobs. and it keeps going. it never starts calculating the
force constants or so. does anyone know what could be the problem? is the
solvent method i'm uasing the cause for this? is in any way possible to
get the free energy in solvent (that's the reason i'm doing a frequency
job).
Thank you very much.
Sincerely,
Liviu Mirica




**************************
Liviu Mihail Mirica			tel: 650-497-3188
Escondido Village, 35 B			email: liviu=at=leland.stanford.edu
Stanford, CA 94305, USA



From chemistry-request@ccl.net Tue Apr 27 17:52:01 2004
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Date: Tue, 27 Apr 2004 15:53:18 -0700 (PDT)
From: "S.I.Gorelsky" <gorelsky(at)stanford.edu>
To: chemistry(at)ccl.net
Subject: charge decomposition analysis with AOMix-CDA
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Hello,
the update for AOMix-CDA is available.

AOMix-CDA performs the MO decomposition analysis in terms of fragment
molecular orbitals (FMOs) and calculates the amount of electron donation,
back-donation and repulsion between molecular fragments (based on
the idea of G. Frenking and co-workers). For ZDO (zero differential
overlap) calculations, AOMix-CDA employs another scheme (to be published)
to calculate donation and back-donation between molecular fragments).

AOMix-CDA can be used for both spin-restricted and spin-unrestricted
calculations. You can also process "mixed type" calculations such as, for
example, the whole molecule is treated at the spin-unrestricted level
while one or all of the molecular fragments are treated at the
spin-restricted level.

The number of fragments is not limited to two. In the current version, the
limit is set to 9. However, this is a rather artificial limitation and
can be removed, so that the program would handle more fragments.

AOMix-CDA can process HF/DFT wavefunctions from
    ADF 200x
    GAMESS (US)
    Gaussian 98/03
    Jaguar 3.x-5.x calculations
and semiempirical ZDO wavefunctions from
    Gaussian ZINDO
    HyperChem
    Spartan
    Zerner's ZINDO
    and CNDO/INDO (J. Reimers) calculations.

For more information, please visit

http://www.stanford.edu/~gorelsky/software/aomix-s/

With best regards,

S. Gorelsky

----------------------------------------------------------------
 Dr S.I. Gorelsky, Department of Chemistry, Stanford University
 Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA
 Phone: (650) 723-0041. Fax: (650) 723-0553.
----------------------------------------------------------------




From chemistry-request@ccl.net Tue Apr 27 13:09:22 2004
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Date: Tue, 27 Apr 2004 20:28:48 +0200
From: Alessandro Contini <alessandro.contini~at~unimi.it>
Subject: TCP-LINDA on intel xeon cluster
To: chemistry~at~ccl.net
Reply-to: alessandro.contini~at~unimi.it
Message-id: <200404272028.48698.alessandro.contini~at~unimi.it>
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Dear all,
we are trying to install g03 on a 128 nodes dual xeon linux cluster. While the 
single node version of g03 installed successfully, we are experiencing 
troubles with tcp-linda. Here is the log message we get while installing 
Linda:
/home/interni/maucrem/gaussian03/g03/linda7.1/intel-linux2.4/lib/ltcp_linda
. a(largs.o)(.text+0x499): In function `ext_get_arg':
 /sca/homes/daya/linda/ikernel-tcp/largs.c:235: undefined reference to
 `__ctype_b'

Does anybody has any idea about solving this?
Thanks a lot for your help

Alessandro Contini
-- 
Alessandro Contini, Ph.D.
Istituto di Chimica Organica "Alessandro Marchesini"
Universit` degli Studi di Milano, Facolt` di Farmacia
Via Venezian, 21 20133 Milano 
Tel. +390250314480 Fax. +390250314476
e-mail alessandro.contini~at~unimi.it





From chemistry-request@ccl.net Tue Apr 27 09:42:04 2004
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Reply-To: jerome|at|scs.uiuc.edu
From: "Jerome Baudry" <jerome|at|scs.uiuc.edu>
To: chemistry|at|ccl.net
Subject: SUMMARY: secondary struct. to protein models
Date: Tue, 27 Apr 2004 09:41:07 -0500
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Dear list

A couple of weeks ago I asked about ides and references on how to assemble
NMR-obtained secondary structure assignments of protein domains into a
possible ensemble of protein structure(s). Apparently, there is no clear
roadmap to do such a think. Several solutions exist to evaluate the quality
of a protein structure, e.g. Sippl's approaches or Profile3D-like
approaches, but assembling several protein domains into one protein
structure seems to be a field in progress. Work in this direction is based
on protein-protein interaction approaches e.g. FTDOCK and others, and on
threading approaches. I received several good ideas and references. Thanks
to all. I include here a summary of the emails I get.

----------------------------------------------------------
Jerome Baudry, Ph.D.       Senior Research Scientist, VizLab Manager.
School of Chemical Sciences    University of Illinois at Urbana-Champaign
505 S. Mathews Ave.; Box 2.1; Urbana, IL, 61801
 Phone: (1) (217) 244 3210; Fax: (1) (217) 333 3120;    e-mail:
jerome|at|scs.uiuc.edu

==== SUMMARY ===

You may want to have a look a Dobrodumov and Gronenborn (2003) Proteins:
Structure, Function, and Genetics 52, 18-32. In order to apply their
approach, you
will need to measure RDC data for the intact protein.
Keith Constantine, BMS
====

Have a look at "Multiscale Modeling Tools in Structural Biology" tool set:
http://mmtsb.scripps.edu/. It allows you to pass to lattice description of
the protein, fix the secondary structure elements and run minimization by
replica exchange algorithm. The final low-energy conformations can be
converted back to atomistic models and, possibly, refined by using more
realistic force field/solvation schemes (say CHARMM22 + GBSA).
Andriy Baumketner, UCSB
====

I do not know of a program that could do what you are proposing,
although we have been thinking of automating such a process
with our combinatorial stochastic elimination algorithm (PNAS 99, 703
(2002)).
In the meantime, it seems to me that you could possibly get a few
alternatives by running MD with constraints on your secondary structure
elements, in various temperatures, and "cool down" by simulated annealing
or by regular minimization, at many different points along the MD.
Amiram Goldblum, Hebrew University

====
Looking at this problem from another perspective, maybe you don't need to
generate models and evaluate them. Have you thought about doing some sort of
'threading' with your sequence of secondary structure elements? Find the
known structures could be compatible with what you know about the sequence
of secondary structure elements? Such threading should recognize structural
homology where sequence homology was not high enough to detect.
You might be able to use existing sequence alignment tools, but use a
sequence that says, HHHHTTTTSSSSSSSSSSSRRRHHHHHHHHH, etc. Generate a
template from your information and a library from the pdb. The advantage of
using sequence alignment software is that it will already know about gaps,
insertions and deletions in generating a score.
Jeff Bell, Accelrys

====
How about a PMF derived from a statistical analysis of the information? This
could be easily represented as a scoring function. I think a full potential
energy function is overkill for this. A good source of information would be
papers on PMF's for threading my people like Manfred Sippl, Jeff Skolnick,
Adam Godzik, etc. In its essence, this is very much the kind of information
fold recognition programs use, except that they analyse pdb structures.
Programs like David Eisenberg's SeqFold, essentially do fold recognition
using secondary structure.
Deepak Singh (Accelrys)

+ thanks to UCSD's Stewart Adcok for information about his lab's current
work in this field.





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Date: Wed, 28 Apr 2004 09:59:47 +1200
From: pdw.boyd|at|auckland.ac.nz
To: chemistry|at|ccl.net
Subject: X3LYP and Gaussian03
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Hello CCL

Has anyone figured out how to use the X3LYP extended density functional 
recently reported by Xu and Goddard (PNAS 101,2673,2004) within Gaussian 03.
In the user defined Model section of the G03 manual it is not clear how to 
incorporate both the B88 and PW91 exchange functionals as prescribed in this 
paper using the Iop non standard options.

Thanks

Peter Boyd
Chemistry Department
The University of Auckland
Auckland
New Zealand



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