From owner-chemistry@ccl.net Tue Mar 21 03:43:00 2006
From: "Ramon Crehuet rcsqtc^iiqab.csic.es" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: How to select residues
Message-Id: <-31253-060321033903-20736-GrLzU+N0/v4gWg7BmapThQ ~ server.ccl.net>
X-Original-From: Ramon Crehuet <rcsqtc _ iiqab.csic.es>
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Date: Tue, 21 Mar 2006 09:40:25 +0100
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Sent to CCL by: Ramon Crehuet [rcsqtc!A!iiqab.csic.es]
Hi Nicolas,
You can use VMD. A sentence like this would show the selected residues:
same residue as within 4 of XXX
that would select any residue that has one or more atoms at 4 ansgstroms 
> from XXX, where XXX is the name of an atom, a resdidue, etc.
I don't remember how to do it right now, but you can also save selections.
Cheers,
Ramon



Nicolas Ferre nicolas.ferre*univ-provence.fr wrote:

>Sent to CCL by: "Nicolas  Ferre" [nicolas.ferre]^[univ-provence.fr]
>Dear CCL'ers,
>
>I'd like to select and save a small part of a pdb file. Actually I want to select all the residues inside a given sphere centered on an amino-acid.
>I know I can use RasMol's "select within (expression)" but it results in selecting some atoms, not whole amino-acids. Obviously I can look at the selection using "show selected" and copy/paste every amino-acid label, but this is a rather tedious task.
>Alternatively I can use Molden, but as far as I known, it only shows the corresponding amino-acids without giving the possibility to save them in a file.
>If I am wrong, please correct me. If not, do you know any free software allowing such residue selection and saving ?
>
>Best regards,
>
>Nicolas>
>
>
>
>  
>


From owner-chemistry@ccl.net Tue Mar 21 05:14:00 2006
From: "Roger Kevin Robinson r.robinson]^[imperial.ac.uk" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Scan
Message-Id: <-31254-060321051306-20649-VFPmwo7j3vq4oXMs2HPLpw===server.ccl.net>
X-Original-From: Roger Kevin Robinson <r.robinson/a\imperial.ac.uk>
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Sent to CCL by: Roger Kevin Robinson [r.robinson[]imperial.ac.uk]

>Hi,
>
>    Im trying to rotate the methyl group on CH2CCH3 using the scan 
>option. My input file is listed below. I've associated the hydrogens on 
>the methyl together and then tried to rotate it. However I dont think 
>the group is completely rotated because the results I am getting do not 
>show a high enough change in energy and because it just looks wrong when 
>I load the .log file into gaussview. Can any one tell me what im doing 
>wrong ?
>
>Thansk Roger
>
>%chk=/home2/rkr79/gaussian/C7H7OO/scans/t-C3H51.chk
>%mem=6MW
>%nproc=1
># scan ub3lyp/6-31g(d,p) geom=connectivity
>
>Title Card Required
>
>0 2
> C
> H                  1              B1
> H                  1              B2    2              A1
> C                  1              B3    3              A2    
>2              D1
> C                  4              B4    1              A3    
>3              D2
> H                  5              B5    4              A4    
>1              D3
> H                  5              B6    4              A5    
>6              D4
> H                  5              B7    4              A6    
>6              D5
>
>   B1             1.07947785
>   B2             1.07429198
>   B3             1.32536491
>   B4             1.48887310
>   B5             1.08760730
>   B6             1.08476175
>   B7             1.08474310
>   A1           116.55338488
>   A2           121.66621285
>   A3           136.00396434
>   A4           110.81891406
>   A5           110.80676392
>   A6           110.80788943
>   D1          -179.97841932
>   D2          -179.94904922
>   D3            -0.70235405 s 23 15.0
>   D4           119.49414900
>   D5          -120.86797802
>
> 1 2 1.0 3 1.0 4 2.0
> 2
> 3
> 4 5 1.0
> 5 6 1.0 7 1.0 8 1.0
> 6
> 7
> 8
>
>
>
>
>  
>


From owner-chemistry@ccl.net Tue Mar 21 06:01:00 2006
From: "J.Aires de Sousa jas^fct.unl.pt" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Workshop "Chemoinformatics in Europe: Research and Teaching"
Message-Id: <-31255-060321055856-13703-rcRRmzEPqNgFcY5EVzbQ2Q(!)server.ccl.net>
X-Original-From: "J.Aires de Sousa" <jas%%fct.unl.pt>
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Date: Tue, 21 Mar 2006 10:58:41 +0000
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Sent to CCL by: "J.Aires de Sousa" [jas*|*fct.unl.pt]


-------- Original Message --------
Subject: 	Workshop "Chemoinformatics in Europe: Research and Teaching "
Date: 	Tue, 21 Mar 2006 11:54:26 +0100
> From: 	Alexandre Varnek <varnek:_:chimie.u-strasbg.fr>

Dear colleague,

You are cordially invited to participate in the Workshop
"Chemoinformatics in Europe: Research and Teaching "  which
will be held in Obernai (near Strasbourg), France, 29 May - 1 June 2006

The program of the workshop includes 4 half-day scientific sessions, a
poster session and a general discussion at the end of the workshop.
The following main topics are selected for the scientific sessions:

1. Encoding chemical structures (safe exchange of information, descriptors,
fingerprints, pharmacophores).
2. Databases and data sources.
3. Property predictions (ADME, environmental related applications).
4. "In silico" design of new compounds (virtual combinatorial libraries,
similarity search).
5. Drug design: Linking chemo- and bio-informatics.
6.Teaching: chemoinformatics in graduate and undergraduate curricula.

Round Table devoted to further development of the European network on
chemoinformatics will be organised at the end of the afternoon session on 31
May. The questions related to organisation of regular workshops and summer
schools in this field will be discussed.


The plenary lectures will be delivered by J. Gasteiger (Univ. of Erlangen,
Germany), P. Willett (Univ. of Sheffield, UK), G. Cruciani (Univ. of
Perugia, Italy), R. Glen (UCMSI, Cambridge, UK), G. Schneider (Univ. of
Frankfurt, Germany), A. Tropsha (Univ. Noth Caroline, USA) and T. Oprea
(Univ. New Mexico, USA).

Detailed information and the registration form are available at
http://infochim.u-strasbg.fr/recherche/europeen_chemistry/index.php


A collection of papers from this meeting is supposed to be published in the
special issue of the journal "Molecular Diversity".

Please note: the number of places in the vilage of vacation "Les Géraniums"
in Obernai is very limited. A "first come, first serve" policy will be
applied, so be sure to submit your application form as soon as possible.

*The deadline for the registration and abstracts submission is April 1.*


Welcome to Obernai !



***********************************
Alexandre Varnek,
Professeur,
Faculté de Chimie,
Université Louis Pasteur,
4, rue B. Pascal,
Strasbourg 67000
FRANCE

tel. +33- 3.90.24.15.60
FAX +33-3.90.24.15.89
e-mail: varnek:_:chimie.u-strasbg.fr
URL: http://infochimie.u-strasbg.fr/
***********************************


From owner-chemistry@ccl.net Tue Mar 21 07:20:00 2006
From: "Pablo Echenique Robba pnique#%#unizar.es" <owner-chemistry]^[server.ccl.net>
To: CCL
Subject: CCL:G: Negative file size in Gaussian03
Message-Id: <-31256-060321070702-10888-jJeaYDk1EF2KHbBnoRYBSw]^[server.ccl.net>
X-Original-From: Pablo Echenique Robba <pnique]|[unizar.es>
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Sent to CCL by: Pablo Echenique Robba [pnique%unizar.es]
Dear CCLers,

I am doing an energy single-point CCSD/cc-pVTZ calculation in Gaussian03 
on the molecule HCO-L-Ala-NH2. The memory and disk limits (1Gb and 50Gb, 
respectively) have been explicitly set.

I get two warnings/errors that distress me, they are consecutive:

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

 **** Warning!!: The largest alpha MO coefficient is  0.11917916D+02

 Estimate disk for full transformation  -868705896 words.
 Semi-Direct transformation.
 Bad length for file.

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

I have found in some old CCL posts that the first warning may be 
prevented to bomb out by specifying the option IOp(8/11=1).

The negative size of the file is, however, critical. After that, of 
course, Gaussian bombs out.

Any idea?

Thanks in advance,

  Pablo Echenique

-- 

------------------------------------
  Pablo Echenique Robba

  Departamento de Fisica Teorica
                &
  Instituto de Biocomputacion y
  Fisica de los Sistemas Complejos
  BIFI

  Universidad de Zaragoza
  50009 Zaragoza
  Spain

  Tel.:    34 976761260
  E-mail:  pnique|,|unizar.es
------------------------------------


From owner-chemistry@ccl.net Tue Mar 21 08:29:00 2006
From: "Jun Cui juc9+^pitt.edu" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: TTM2-F implementation
Message-Id: <-31257-060320034138-12345-T79+31KDHsUPoTN12efp0w[A]server.ccl.net>
X-Original-From: Jun Cui <juc9+_+_pitt.edu>
Date: Mon, 20 Mar 2006 17:31:05 -0500 (EST)
MIME-version: 1.0


Sent to CCL by: Jun Cui [juc9+{:}pitt.edu]
As far as I know, there is no publicly available programs for TTM2-F. 
The author of TTM2-F has a program to implement this force field. You 
may contact with the author to try your luck.

Cheers,

Jun

On Mon, 20 Mar 2006, Rafael R. Pappalardo rafapa#,#us.es wrote:

> Sent to CCL by: "Rafael R. Pappalardo" [rafapa,+,us.es]
> Does anybody knows if there is any publicly available programs which implements the TTM2-F water force field?
> Thanks in advance.
>
> Dr. Rafael R. Pappalardo
> Dept. of Physical Chemistry, Univ. of Seville (Spain)
>


From owner-chemistry@ccl.net Tue Mar 21 09:27:00 2006
From: "Jim Kress ccl_nospam**kressworks.com" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: TTM2-F implementation
Message-Id: <-31258-060321092113-4164-PoA741hwPMWu7asMOFc8JQ]*[server.ccl.net>
X-Original-From: "Jim Kress" <ccl_nospam%a%kressworks.com>
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Sent to CCL by: "Jim Kress" [ccl_nospam-#-kressworks.com]
Try here:

http://www.emsl.pnl.gov/proj/tms/ttm2-r/

Google is a wonderful tool ...

Jim
 

> -----Original Message-----
> From: Jun Cui juc9+^pitt.edu [mailto:owner-chemistry(!)ccl.net] 
> Sent: Tuesday, March 21, 2006 8:35 AM
> To: Kress, Jim 
> Subject: CCL: TTM2-F implementation
> 
> Sent to CCL by: Jun Cui [juc9+{:}pitt.edu] As far as I know, 
> there is no publicly available programs for TTM2-F. 
> The author of TTM2-F has a program to implement this force 
> field. You may contact with the author to try your luck.
> 
> Cheers,
> 
> Jun
> 
> On Mon, 20 Mar 2006, Rafael R. Pappalardo rafapa#,#us.es wrote:
> 
> > Sent to CCL by: "Rafael R. Pappalardo" [rafapa,+,us.es] 
> Does anybody 
> > knows if there is any publicly available programs which 
> implements the TTM2-F water force field?
> > Thanks in advance.
> >
> > Dr. Rafael R. Pappalardo
> > Dept. of Physical Chemistry, Univ. of Seville (Spain)
> >
> 
> 
> 
> -= This is automatically added to each message by the mailing 
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From owner-chemistry@ccl.net Tue Mar 21 10:01:00 2006
From: "Vlad Cojocaru Vlad.Cojocaru=eml-r.villa-bosch.de" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: description of the $VEC group in GAMESS
Message-Id: <-31259-060321094802-21643-v1U8dJUBFeDs+yV8EKi3+Q_+_server.ccl.net>
X-Original-From: Vlad Cojocaru <Vlad.Cojocaru!^!eml-r.villa-bosch.de>
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Sent to CCL by: Vlad Cojocaru [Vlad.Cojocaru:+:eml-r.villa-bosch.de]
Dear CCL-ers,

Does anyone have any idea where I could find a good description of the
$VEC group in GAMESS? Unfortunately the GAMESS documentation lacks such
a description ... And therefore I am having problems in assigning the
correct NORB value in the input file (GUESS=MOREAD) ...

Thanks
vlad

-- 
Dr. Vlad Cojocaru
EML Research gGmbH
Molecular and Cellular Modeling Group
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg, Germany
Phone: +49-6221-533266
Fax: +49-6221-533298
e-mail: Vlad.Cojocaru]~[eml-r.villa-bosch.de
http://projects.villa-bosch.de/mcm/people/cojocaru/


From owner-chemistry@ccl.net Tue Mar 21 10:36:00 2006
From: "Van Dam, HJJ \(Huub\) h.j.j.vandam---dl.ac.uk" <owner-chemistry^-^server.ccl.net>
To: CCL
Subject: CCL:G: Negative file size in Gaussian03
Message-Id: <-31260-060321100103-27675-Niv0i8tMq1681w7S+NdZMw^-^server.ccl.net>
X-Original-From: "Van Dam, HJJ \(Huub\)" <h.j.j.vandam###dl.ac.uk>
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Sent to CCL by: "Van Dam, HJJ \(Huub\)" [h.j.j.vandam!A!dl.ac.uk]
Hi Pablo,

The negative file size suggests in an integer overflow to me (I am not a Gaussian user so I am making a guess here). I.e. the true file size is so large it cannot be represented as a 32 bit integer and as a result the value actually overwrites the sign bit. To me it seems your 2-electron integral file is going to be too big. Please have a look how many orbitals you have (call this number N) and consider that you may need to store N**4 (N to the fourth power) integrals (where 1 integral takes at least 8 bytes). Is that an amount of data you think you can store?

Best wishes,

    Huub

-----Original Message-----
> From: owner-chemistry#,#ccl.net [mailto:owner-chemistry#,#ccl.net]
Sent: 21 March 2006 12:43
To: Vandam, Huub 
Subject: CCL:G: Negative file size in Gaussian03


Sent to CCL by: Pablo Echenique Robba [pnique%unizar.es]
Dear CCLers,

I am doing an energy single-point CCSD/cc-pVTZ calculation in Gaussian03 
on the molecule HCO-L-Ala-NH2. The memory and disk limits (1Gb and 50Gb, 
respectively) have been explicitly set.

I get two warnings/errors that distress me, they are consecutive:

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

 **** Warning!!: The largest alpha MO coefficient is  0.11917916D+02

 Estimate disk for full transformation  -868705896 words.
 Semi-Direct transformation.
 Bad length for file.

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

I have found in some old CCL posts that the first warning may be 
prevented to bomb out by specifying the option IOp(8/11=1).

The negative size of the file is, however, critical. After that, of 
course, Gaussian bombs out.

Any idea?

Thanks in advance,

  Pablo Echenique

-- 

------------------------------------
  Pablo Echenique Robba

  Departamento de Fisica Teorica
                &
  Instituto de Biocomputacion y
  Fisica de los Sistemas Complejos
  BIFI

  Universidad de Zaragoza
  50009 Zaragoza
  Spain

  Tel.:    34 976761260
  E-mail:  pnique-$-unizar.es
------------------------------------http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Tue Mar 21 11:11:00 2006
From: "Florian Haberl Florian.Haberl[#]chemie.uni-erlangen.de" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: How to select residues
Message-Id: <-31261-060321100741-539-BSd8U1Mt5/y4jspX7c3bew:-:server.ccl.net>
X-Original-From: Florian Haberl <Florian.Haberl*chemie.uni-erlangen.de>
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Sent to CCL by: Florian Haberl [Florian.Haberl[A]chemie.uni-erlangen.de]
hi,

On Monday 20 March 2006 22:19, Nicolas Ferre nicolas.ferre*univ-provence.fr 
wrote:
> Sent to CCL by: "Nicolas  Ferre" [nicolas.ferre]^[univ-provence.fr]
> Dear CCL'ers,
>
> I'd like to select and save a small part of a pdb file. Actually I want to
> select all the residues inside a given sphere centered on an amino-acid. I
> know I can use RasMol's "select within (expression)" but it results in
> selecting some atoms, not whole amino-acids. Obviously I can look at the
> selection using "show selected" and copy/paste every amino-acid label, but
> this is a rather tedious task. Alternatively I can use Molden, but as far
> as I known, it only shows the corresponding amino-acids without giving the
> possibility to save them in a file. If I am wrong, please correct me. If
> not, do you know any free software allowing such residue selection and
> saving ?

Also swisspdb viewer ( http://www.expasy.org/spdbv/text/download.htm )   can 
do this:

Select - neighbors of selected aa:
Within distance

If you want to do this with multiple files (for example: You want all aa 
around a ligand),  you can use something like perlmol 
(to be found on: http://www.perlmol.org/ )

and than the module: midas pattern

There`s also a solution for python i think its`s called mdtools 
(http://www.ks.uiuc.edu/Development/MDTools/ )
and some other molecular toolkits around.


Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------


From owner-chemistry@ccl.net Tue Mar 21 11:46:00 2006
From: "Daniel Schofield dan++visual1.chem.pitt.edu" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL: TTM2-F implementation
Message-Id: <-31262-060320231616-5517-5P0hKaxntCC3PP9YY7HOnQ*|*server.ccl.net>
X-Original-From: Daniel Schofield <dan()visual1.chem.pitt.edu>
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Date: Mon, 20 Mar 2006 15:24:27 -0500
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Sent to CCL by: Daniel Schofield [dan%a%visual1.chem.pitt.edu]

Hi Rafael
Check
http://www.pnl.gov/chemistry/highlights/water_potential.stm
a Fortran-90 subroutine with the new version of the TTM2.1-F potential  
(energies and gradients).

If you haven't seen it, you might also be interested in reading

The Flexible, Polarizable, Thole-Type Interaction Potential for Water  
(TTM2-F) Revisited
George S. Fanourgakis and Sotiris S. Xantheas
J. Phys. Chem. A 2006, 110, 4100-4106

Daniel


On Mon, 20 Mar 2006 14:55:39 -0500, Rafael R. Pappalardo rafapa#,#us.es  
<owner-chemistry/a\ccl.net> wrote:

> Sent to CCL by: "Rafael R. Pappalardo" [rafapa,+,us.es]
> Does anybody knows if there is any publicly available programs which  
> implements the TTM2-F water force field?
> Thanks in advance.
>
> Dr. Rafael R. Pappalardo
> Dept. of Physical Chemistry, Univ. of Seville (Spain)>
>


From owner-chemistry@ccl.net Tue Mar 21 12:21:01 2006
From: "Joe Corkery jcorkery(!)eyesopen.com" <owner-chemistry%server.ccl.net>
To: CCL
Subject: CCL: How to select residues
Message-Id: <-31263-060321092218-4670-M2HCwVEcpP+IeOo9J5DctA%server.ccl.net>
X-Original-From: Joe Corkery <jcorkery:-:eyesopen.com>
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Sent to CCL by: Joe Corkery [jcorkery^eyesopen.com]
Hi Nicolas,

This can be done in OpenEye's VIDA application (which is free for non- 
commercial use). To do this, first select the desired amino acid.  
Second, go to the "Molecules" page of the Style Control and adjust  
the "selection" slider such that the numeric display next to it shows  
the desired number of Angstroms that you want to select within. You  
will also see a transparent white "halo" around the original amino  
acid which shows you all of the atoms within that region. There is a  
button next to the slider which toggles the display such that only  
things within the halo are displayed (note that if an atom is within  
the halo, the entire amino acid containing that atom is displayed).  
Once you are satisfied, there is a "Select Within" button above the  
slider which will allow you to select all of the atoms within this  
range.

Once you have selected this set (you can also do all of this from a  
Python scripting command if desired), go to the Edit menu and select  
the "Split Molecules" option which contains three sub-options, choose  
"Selected". This will create a new molecule containing only those  
selected atoms and bonds. You can then save this new molecule out to  
disk. Another option in the "Split Molecules" submenu "Components"  
splits up the molecule into its expected components (i.e. it  
separates ligands from individual chains from waters from  metals). I  
hope that this helps.

The Python scripting command is:

SelectWithin(radius, selected)

Where radius is the range in Angstroms and selected corresponds to  
whether you wish to select or unselect the resulting atom sets. Again  
this does residue expansion. This function expects that there is  
already another set of atoms/bonds selected from which to apply the  
radius to.

Joe Corkery


On Mar 20, 2006, at 4:25 PM, Nicolas Ferre nicolas.ferre*univ- 
provence.fr wrote:

> Sent to CCL by: "Nicolas  Ferre" [nicolas.ferre]^[univ-provence.fr]
> Dear CCL'ers,
>
> I'd like to select and save a small part of a pdb file. Actually I  
> want to select all the residues inside a given sphere centered on  
> an amino-acid.
> I know I can use RasMol's "select within (expression)" but it  
> results in selecting some atoms, not whole amino-acids. Obviously I  
> can look at the selection using "show selected" and copy/paste  
> every amino-acid label, but this is a rather tedious task.
> Alternatively I can use Molden, but as far as I known, it only  
> shows the corresponding amino-acids without giving the possibility  
> to save them in a file.
> If I am wrong, please correct me. If not, do you know any free  
> software allowing such residue selection and saving ?
>
> Best regards,
>
> Nicolas
>
>
>
> -= This is automatically added to each message by the mailing  
> script =-
> To recover the email address of the author of the message, please  
> change> Conferences: http://server.ccl.net/chemistry/announcements/ 
> conferences/
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From owner-chemistry@ccl.net Tue Mar 21 12:57:01 2006
From: "Richard M. Casey rcasey ~~ rmcbiosciences.com" <owner-chemistry#%#server.ccl.net>
To: CCL
Subject: CCL: current protocols
Message-Id: <-31264-060321121958-29257-HUxe212LcWIrK3mOVXVbIA#%#server.ccl.net>
X-Original-From: "Richard M. Casey" <rcasey],[rmcbiosciences.com>
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Date: Tue, 21 Mar 2006 10:20:05 -0700
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Sent to CCL by: "Richard M. Casey" [rcasey^^^rmcbiosciences.com]
This is a multi-part message in MIME format.

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Andy,

I think this is an excellent idea.........

Regards,
Richard Casey
RMC Biosciences, Inc.


=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Afternoon all,
   For the past couple of weeks, I have been kicking around an idea and =
I would
like some feedback from the larger community.

   Those here who deal with wet biology and biochemistry or =
bioinformatics have
probably come in contact with the Current Protocols series.  For those =
who
aren't familiar with it, Current Protocols is a set of loose-leaf =
reference
volumes ( or their electronic equivalent) that provide a standard method =
for
common lab operations and enough of the theory behind it.  They have a =
volume
for bioinformatics as well, with articles such as "Multiple Sequence =
Alignment
using ClustalW and ClustalX". The website, for those who are interested =
is
http://www.currentprotocols.com .

    My question/proposal is simple.  Has the time come for the =
computational
chemistry community to have a similar resource available?  I don't =
necessarily
think that this need be a volume in the aforementioned series, but =
someplace
that someone needing to perform a calculation that they aren't familiar =
with can
go to get a sense of what others would consider the "right" way to do =
it.

So, what say ye?  Would this be considered useful, and, more to the =
point, are
there any practitioners out there who are interested in talking in more =
depth
about what form and content this project could take on?

Thanks,
Andy

--=20
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant#,#pobox.com | That shines on me               | Disclaimer:  I =
don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myself


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<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
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<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Andy,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>I think this is an excellent=20
idea.........</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Regards,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Richard Casey</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>RMC Biosciences, Inc.</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman"=20
size=3D3></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman"=20
size=3D3></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial =
size=3D2>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D</FONT></DIV>
<DIV><FONT face=3DArial size=3D2><FONT face=3D"Times New Roman" =
size=3D3>Afternoon=20
all,<BR>&nbsp;&nbsp; For the past couple of weeks, I have been kicking =
around an=20
idea and I would<BR>like some feedback from the larger=20
community.<BR><BR>&nbsp;&nbsp; Those here who deal with wet biology and=20
biochemistry or bioinformatics have<BR>probably come in contact with the =
Current=20
Protocols series.&nbsp; For those who<BR>aren't familiar with it, =
Current=20
Protocols is a set of loose-leaf reference<BR>volumes ( or their =
electronic=20
equivalent) that provide a standard method for<BR>common lab operations =
and=20
enough of the theory behind it.&nbsp; They have a volume<BR>for =
bioinformatics=20
as well, with articles such as "Multiple Sequence Alignment<BR>using =
ClustalW=20
and ClustalX". The website, for those who are interested is<BR></FONT><A =

href=3D"http://www.currentprotocols.com"><FONT face=3D"Times New Roman"=20
size=3D3>http://www.currentprotocols.com</FONT></A><FONT face=3D"Times =
New Roman"=20
size=3D3> .<BR><BR>&nbsp;&nbsp;&nbsp; My question/proposal is =
simple.&nbsp; Has=20
the time come for the computational<BR>chemistry community to have a =
similar=20
resource available?&nbsp; I don't necessarily<BR>think that this need be =
a=20
volume in the aforementioned series, but someplace<BR>that someone =
needing to=20
perform a calculation that they aren't familiar with can<BR>go to get a =
sense of=20
what others would consider the "right" way to do it.<BR><BR>So, what say =

ye?&nbsp; Would this be considered useful, and, more to the point, =
are<BR>there=20
any practitioners out there who are interested in talking in more =
depth<BR>about=20
what form and content this project could take=20
on?<BR><BR>Thanks,<BR>Andy<BR><BR>-- <BR>Andrew Fant&nbsp;&nbsp;&nbsp; | =
And=20
when the night is cloudy&nbsp;&nbsp;&nbsp; | This space to =
let<BR>Molecular Geek=20
| There is still a =
light&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
|----------------------<BR>fant#,#pobox.com | That shines on=20
me&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;=20
| Disclaimer:&nbsp; I don't<BR>Boston, MA&nbsp;&nbsp;&nbsp;&nbsp; | =
Shine until=20
tomorrow, Let it be | even speak for=20
myself</FONT><BR><BR></DIV></FONT></BODY></HTML>

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From owner-chemistry@ccl.net Tue Mar 21 13:31:00 2006
From: "=?ISO-8859-1?Q?Francisco_Partal_Ure=F1a?= fpartal**ujaen.es" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian Scan
Message-Id: <-31265-060321065924-10030-XhWfgZGmbWKvyOrJiHYGhw**server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Francisco_Partal_Ure=F1a?= <fpartal]^[ujaen.es>
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Date: Tue, 21 Mar 2006 11:54:58 +0100
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Sent to CCL by: =?ISO-8859-1?Q?Francisco_Partal_Ure=F1a?= [fpartal=-=ujaen.es]
This is a multi-part message in MIME format.
--------------080406020201060007020808
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    Hi Roger: In order to associate the hydrogens on the methyl group 
together, D4 and D5 must be 'normal angles' related to H1 and not 
torsions. At the end of the line in the Z-matrix you must write the 
number 1 to indicate Gaussian this last parameter  is an angle and not a 
torsion.
    Good luck!!


Roger Kevin Robinson r.robinson]^[imperial.ac.uk wrote:

>Sent to CCL by: Roger Kevin Robinson [r.robinson[]imperial.ac.uk]
>
>  
>
>>Hi,
>>
>>   Im trying to rotate the methyl group on CH2CCH3 using the scan 
>>option. My input file is listed below. I've associated the hydrogens on 
>>the methyl together and then tried to rotate it. However I dont think 
>>the group is completely rotated because the results I am getting do not 
>>show a high enough change in energy and because it just looks wrong when 
>>I load the .log file into gaussview. Can any one tell me what im doing 
>>wrong ?
>>
>>Thansk Roger
>>
>>%chk=/home2/rkr79/gaussian/C7H7OO/scans/t-C3H51.chk
>>%mem=6MW
>>%nproc=1
>># scan ub3lyp/6-31g(d,p) geom=connectivity
>>
>>Title Card Required
>>
>>0 2
>>C
>>H                  1              B1
>>H                  1              B2    2              A1
>>C                  1              B3    3              A2    
>>2              D1
>>C                  4              B4    1              A3    
>>3              D2
>>H                  5              B5    4              A4    
>>1              D3
>>H                  5              B6    4              A5    
>>6              D4
>>H                  5              B7    4              A6    
>>6              D5
>>
>>  B1             1.07947785
>>  B2             1.07429198
>>  B3             1.32536491
>>  B4             1.48887310
>>  B5             1.08760730
>>  B6             1.08476175
>>  B7             1.08474310
>>  A1           116.55338488
>>  A2           121.66621285
>>  A3           136.00396434
>>  A4           110.81891406
>>  A5           110.80676392
>>  A6           110.80788943
>>  D1          -179.97841932
>>  D2          -179.94904922
>>  D3            -0.70235405 s 23 15.0
>>  D4           119.49414900
>>  D5          -120.86797802
>>
>>1 2 1.0 3 1.0 4 2.0
>>2
>>3
>>4 5 1.0
>>5 6 1.0 7 1.0 8 1.0
>>6
>>7
>>8>
>
>
>
>  
>

--------------080406020201060007020808
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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<head>
  <meta http-equiv="Content-Type" content="text/html;charset=ISO-8859-1">
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</head>
<body text="#000000" bgcolor="#ffffff">
&nbsp;&nbsp;&nbsp; Hi Roger: In order to associate the hydrogens on the methyl group
together, D4 and D5 must be 'normal angles' related to H1 and not
torsions. At the end of the line in the Z-matrix you must write the
number 1 to indicate Gaussian this last parameter&nbsp; is an angle and not
a torsion.<br>
&nbsp;&nbsp;&nbsp; Good luck!!<br>
<br>
<br>
Roger Kevin Robinson r.robinson]^[imperial.ac.uk wrote:<br>
<blockquote type="cite"
 cite="mid-id%233k5-31254-060321051306-20649-BXf4oXJGMLJqud5nvITAFA-*-server.ccl.net">
  <pre wrap="">Sent to CCL by: Roger Kevin Robinson [r.robinson[]imperial.ac.uk]

  </pre>
  <blockquote type="cite">
    <pre wrap="">Hi,

   Im trying to rotate the methyl group on CH2CCH3 using the scan 
option. My input file is listed below. I've associated the hydrogens on 
the methyl together and then tried to rotate it. However I dont think 
the group is completely rotated because the results I am getting do not 
show a high enough change in energy and because it just looks wrong when 
I load the .log file into gaussview. Can any one tell me what im doing 
wrong ?

Thansk Roger

%chk=/home2/rkr79/gaussian/C7H7OO/scans/t-C3H51.chk
%mem=6MW
%nproc=1
# scan ub3lyp/6-31g(d,p) geom=connectivity

Title Card Required

0 2
C
H                  1              B1
H                  1              B2    2              A1
C                  1              B3    3              A2    
2              D1
C                  4              B4    1              A3    
3              D2
H                  5              B5    4              A4    
1              D3
H                  5              B6    4              A5    
6              D4
H                  5              B7    4              A6    
6              D5

  B1             1.07947785
  B2             1.07429198
  B3             1.32536491
  B4             1.48887310
  B5             1.08760730
  B6             1.08476175
  B7             1.08474310
  A1           116.55338488
  A2           121.66621285
  A3           136.00396434
  A4           110.81891406
  A5           110.80676392
  A6           110.80788943
  D1          -179.97841932
  D2          -179.94904922
  D3            -0.70235405 s 23 15.0
  D4           119.49414900
  D5          -120.86797802

1 2 1.0 3 1.0 4 2.0
2
3
4 5 1.0
5 6 1.0 7 1.0 8 1.0
6
7
8




 

    </pre>
  </blockquote>
  <pre wrap=""><!----E-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY-*-ccl.net">CHEMISTRY-*-ccl.net</a> or use:
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From owner-chemistry@ccl.net Tue Mar 21 14:07:00 2006
From: "Judith Bandy jbandy*o*inforsense.com" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: SECOND ANNOUNCEMENT: InforSense Users Conference Agenda Posted
Message-Id: <-31266-060321121811-25834-FWHsQgjQQQredKzFaQQKUQ_+_server.ccl.net>
X-Original-From: "Judith  Bandy" <jbandy]|[inforsense.com>
Date: Tue, 21 Mar 2006 12:18:09 -0500


Sent to CCL by: "Judith  Bandy" [jbandy]=[inforsense.com]
SECOND ANNOUNCEMENT: Inforsense Users Conference
April 6-7 2006, Boston, USA

Dear Colleague, 
The first InforSense Users Conference, to be held on April 6-7 2006, in Boston, Massachusetts, USA, is now just two weeks away.  If you have not already registered for this exciting and informative event, we are very pleased to invite you to register using the links below.

Our Users Conference will provide you with the opportunity to learn how InforSense KDE is being used to enable business-critical decision making across a variety of industries. You will also have time to network with others in the InforSense community and the chance to provide your input into future integrative analytics product plans.   
 
The Users Conference agenda is now available and features Keynotes and presentations by InforSense users and partners including GlaxoSmithKline, Biogen Idec, Syngenta, Spotfire, Windber Research Institute, and more.  You are invited to a Reception and Partner Integration Showcase highlighting key partner technologies accessible with InforSense KDE.  Attendees can also select Workshops and User Clinics designed to help you to maximize the value of InforSense technology in your organization.  

Please view the Draft Agenda here:
(http://www.inforsense.com/userconference_agenda.html)  

The InforSense Users Conference will take place at the downtown Boston offices of Apple Computer in the Prudential Center.  Attendance is free of charge.

Please register today (http://www.inforsense.com/user_group_meeting.html) to reserve your place and receive further information of this valuable event. If you do not receive registration confirmation or for any other questions, please call Emma Cutting at +44 207 808 9524 or send email to information,+,inforsense.com.  

Event: 
InforSense Users Conference
  
Date and Time: 
Thursday, April 6, 2006 8:00am - 7pm
Friday, April 7, 2006 8:00am - 4pm 

Location: 
Apple  Computer Market Center
111 Huntington Ave., 5th Floor
Boston, MA 02199 USA 
 +1 617 263 7200

_______

InforSense Ltd
+44 207 808 9500

InforSense -  North America 
+1 617 547 2500
 
www.inforsense.com 

 
2006 InforSense Ltd. All rights reserved. InforSense, the InforSense logo and TextSense are registered trade-marks of InforSense Ltd. Open Discovery Workflow is a trademark of InforSense Ltd. All other brands or products names are trademarks of their respective holders


From owner-chemistry@ccl.net Tue Mar 21 16:22:00 2006
From: "Rafael R. Pappalardo rafapa]~[us.es" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: TTM2-F implementation
Message-Id: <-31267-060321121431-19040-kcnvskmehQu0DCQKn1ZR6Q|-|server.ccl.net>
X-Original-From: "Rafael R. Pappalardo" <rafapa * us.es>
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Sent to CCL by: "Rafael R. Pappalardo" [rafapa(a)us.es]
On Tuesday 21 March 2006 16:02, Jim Kress ccl_nospam**kressworks.com wrote:
> Sent to CCL by: "Jim Kress" [ccl_nospam-#-kressworks.com]
> Try here:
>
> http://www.emsl.pnl.gov/proj/tms/ttm2-r/
>
> Google is a wonderful tool ...
>
> Jim

I agree with you about Google. Unfortunately, the page you refers contains 
only the subroutine which define the force field. I was looking a complete MD 
program. Something like, TINKER, GROMACS, DL_POLY, etc.

Thanks anyway,

Rafael
>
> > -----Original Message-----
> > From: Jun Cui juc9+^pitt.edu [mailto:owner-chemistry_-_ccl.net]
> > Sent: Tuesday, March 21, 2006 8:35 AM
> > To: Kress, Jim
> > Subject: CCL: TTM2-F implementation
> >
> > Sent to CCL by: Jun Cui [juc9+{:}pitt.edu] As far as I know,
> > there is no publicly available programs for TTM2-F.
> > The author of TTM2-F has a program to implement this force
> > field. You may contact with the author to try your luck.
> >
> > Cheers,
> >
> > Jun
> >
> > On Mon, 20 Mar 2006, Rafael R. Pappalardo rafapa#,#us.es wrote:
> > > Sent to CCL by: "Rafael R. Pappalardo" [rafapa,+,us.es]
> >
> > Does anybody
> >
> > > knows if there is any publicly available programs which
> >
> > implements the TTM2-F water force field?
> >
> > > Thanks in advance.
> > >
> > > Dr. Rafael R. Pappalardo
> > > Dept. of Physical Chemistry, Univ. of Seville (Spain)
> >
> > -= This is automatically added to each message by the mailing
> > script =- To recover the email address of the author of the
> > message, please change the strange characters on the top line
> > to the _-_ sign. You can also look up the X-Original-From: line
> > in the mail header.> Conferences:
> > http://server.ccl.net/chemistry/announcements/conferences/
> >
> > Search Messages: http://www.ccl.net/htdig  (login: ccl,
> > Password: search)>
> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> > -+-+-+-+-+

From owner-chemistry@ccl.net Tue Mar 21 19:10:00 2006
From: "Wayne Steinmetz WES04747-,-pomona.edu" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Time for a Current Protocols in Computational Chemistry?
Message-Id: <-31268-060321190811-21951-JSD7rJmIzQWjXFC1GEmRUg]~[server.ccl.net>
X-Original-From: "Wayne Steinmetz" <WES04747:+:pomona.edu>
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Sent to CCL by: "Wayne Steinmetz" [WES04747/./pomona.edu]
Yes and no.

I became aware of Current Protocols when I modified our NMR spectrometer
to perform MRI imaging.  I have downloaded helpful material from the
Current Protocol site devoted to MRI.  I looked at the sample protocol
at the Bioinformatics site.  I found it much too mechanical. Click here
and click there and the process works.  Ha!  Serious computational
chemists don't work that way.  A protocol written in that fashion would
be useless at best and probably dangerous.

However, following the MRI example, a discussion of the procedure in the
style of Organic Syntheses would be helpful.  A useful protocol would at
each step discuss the rationale for the step and point out the traps.
In other words, explain what works (and why) and what doesn't work (and
why). 

Wayne E. Steinmetz
Carnegie Professor of Chemistry
Woodbadge Course Director
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz . pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 

-----Original Message-----
> From: owner-chemistry . ccl.net [mailto:owner-chemistry . ccl.net] 
Sent: Monday, March 20, 2006 3:48 PM
To: Wayne Steinmetz
Subject: CCL: Time for a Current Protocols in Computational Chemistry?

Sent to CCL by: "Andrew D. Fant" [fant=pobox.com]
Afternoon all,
   For the past couple of weeks, I have been kicking around an idea and
I would
like some feedback from the larger community.

   Those here who deal with wet biology and biochemistry or
bioinformatics have
probably come in contact with the Current Protocols series.  For those
who
aren't familiar with it, Current Protocols is a set of loose-leaf
reference
volumes ( or their electronic equivalent) that provide a standard method
for
common lab operations and enough of the theory behind it.  They have a
volume
for bioinformatics as well, with articles such as "Multiple Sequence
Alignment
using ClustalW and ClustalX". The website, for those who are interested
is
http://www.currentprotocols.com .

    My question/proposal is simple.  Has the time come for the
computational
chemistry community to have a similar resource available?  I don't
necessarily
think that this need be a volume in the aforementioned series, but
someplace
that someone needing to perform a calculation that they aren't familiar
with can
go to get a sense of what others would consider the "right" way to do
it.

So, what say ye?  Would this be considered useful, and, more to the
point, are
there any practitioners out there who are interested in talking in more
depth
about what form and content this project could take on?

Thanks,
	Andy

-- 
Andrew Fant    | And when the night is cloudy    | This space to let
Molecular Geek | There is still a light          |----------------------
fant#,#pobox.com | That shines on me               | Disclaimer:  I
don't
Boston, MA     | Shine until tomorrow, Let it be | even speak for myselfhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-------------------------------------------------------------
This message has been scanned by Postini anti-virus software.


From owner-chemistry@ccl.net Tue Mar 21 20:53:01 2006
From: "Loan Huynh huynhkl2000{:}yahoo.ca" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: A review of force fields
Message-Id: <-31269-060321203215-22087-Lh9yi+piO4Sj3vi0u1VM3w#server.ccl.net>
X-Original-From: Loan Huynh <huynhkl2000-#-yahoo.ca>
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Date: Tue, 21 Mar 2006 20:32:01 -0500 (EST)
MIME-Version: 1.0


Sent to CCL by: Loan Huynh [huynhkl2000|-|yahoo.ca]
--0-632566050-1142991121=:76758
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

Hi All,
   
  Thank you very much for all of your suggestions for the review papers on the currently used forcefields as well as comments on the used of the force field.  I’ll consider your points and try to read all of the recommend paper and I'll to have a short summarized those papers posted later.
   
  Many thanks,
  LH.
   
  
"Fiona Case fhcase#,#hotmail.com" <owner-chemistry .. ccl.net> wrote:
  Sent to CCL by: "Fiona Case" [fhcase###hotmail.com]
Hello,

I'd like to suggest that you have two questions to answer: Which forcefield 
to use, and which method to use (MD/MC, which flavor?). If you make a wise 
choice of forcefield, but a poor choice of method, you will still get poor 
results.

Also, when you look at many of the "forcefield review" papers they consider 
intramolecular interactions (bond lengths, bond angles, vibrational 
frequencies obtained from isolated molecules, etc.). Unless you are trying 
to predict properties of molecules in a vacuum, intermolecular interations 
are at least as important. Most do not consider the effect of temperature or 
pressure, nor do they provide guidence on the transferability of the 
forcefields (what will happen if your molecule is slightly different to the 
one used in the published study?)

This lack of validation/verification/guidence has been identified as a major 
limitation to the useful application of force field based methods.

http://www.chemicalvision2020.org/pdfs/compchem.pdf

http://fluidproperties.org/Vision-and-Strategic-Plan-5-Feb-06.pdf

However, there is some good news: Some organizations are attempting to solve 
this problem. If you take a look at the publications and websites that have 
resulted from their efforts you will already see some guidence on forcefield 
and method selection for "useful" simulations.

1) The Industrial Fluid Properties Simulation Collective (of which I am a 
member)http://fluidproperties.org/

2) The BioSimGrid, http://www.biosimgrid.org/

3) The protein folding challenges: http://predictioncenter.org/

4) If you are looking at something that is a crystal, see the Crystal 
Structure Prediction challenges: 
http://scripts.iucr.org/cgi-bin/paper?S0108768105016563

You could encourage every "modeling expert" you meet (particularly in 
academia) to support these efforts. The problems you are facing in trying to 
select a forcefield and method to use for your work are shared by everyone 
attempting to apply these methods. It is of benefit to us all that more 
validation/verification/guidence becomes available so that molecular 
simulations methods become "useful" to the wider world, and particularly in 
industry.


Fiona Case


----Original Message Follows----
> From: "Carlos Nunez carlos_javierna*o*yahoo.com" 
Reply-To: "CCL Subscribers" 
To: "Case, Fiona " 
Subject: CCL: A review of force fields
Date: Thu, 16 Mar 2006 20:57:41 -0500

Sent to CCL by: "Carlos Nunez" [carlos_javierna{:}yahoo.com]
Hi,

See this:

MacKerell A. D. Jr. 2004. Empirical force fields for biological
macromolecules: overview and issues. J. Comput. Chem. 25: 1584-1604.


Hasta la proxima vez,
Carlos N.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-632566050-1142991121=:76758
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: 8bit

<div>Hi All,</div>  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"></SPAN>&nbsp;</div><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Thank you very much for all of your suggestions for the review papers on the currently used forcefields as well as comments on the used of the force field.<SPAN style="mso-spacerun: yes">&nbsp; </SPAN>I’ll consider your points and try to read all of the recommend paper and I'll&nbsp;to have&nbsp;a&nbsp;short summarized those papers posted&nbsp;later.</SPAN></div>  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN>&nbsp;</div>  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">Many thanks,<o:p></o:p></SPAN></div>
  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial">LH.<o:p></o:p></SPAN></div>  <div class=MsoNormal style="MARGIN: 0cm 0cm 0pt"><SPAN style="FONT-SIZE: 10pt; FONT-FAMILY: Arial"><SPAN style="mso-spacerun: yes"></SPAN></SPAN></SPAN>&nbsp;</div>  <div><BR><B><I>"Fiona Case fhcase#,#hotmail.com" &lt;owner-chemistry .. ccl.net&gt;</I></B> wrote:</div>  <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">Sent to CCL by: "Fiona Case" [fhcase###hotmail.com]<BR>Hello,<BR><BR>I'd like to suggest that you have two questions to answer: Which forcefield <BR>to use, and which method to use (MD/MC, which flavor?). If you make a wise <BR>choice of forcefield, but a poor choice of method, you will still get poor <BR>results.<BR><BR>Also, when you look at many of the "forcefield review" papers they consider <BR>intramolecular interactions (bond lengths, bond angles, vibrational <BR>frequencies obtained
 from isolated molecules, etc.). Unless you are trying <BR>to predict properties of molecules in a vacuum, intermolecular interations <BR>are at least as important. Most do not consider the effect of temperature or <BR>pressure, nor do they provide guidence on the transferability of the <BR>forcefields (what will happen if your molecule is slightly different to the <BR>one used in the published study?)<BR><BR>This lack of validation/verification/guidence has been identified as a major <BR>limitation to the useful application of force field based methods.<BR><BR>http://www.chemicalvision2020.org/pdfs/compchem.pdf<BR><BR>http://fluidproperties.org/Vision-and-Strategic-Plan-5-Feb-06.pdf<BR><BR>However, there is some good news: Some organizations are attempting to solve <BR>this problem. If you take a look at the publications and websites that have <BR>resulted from their efforts you will already see some guidence on forcefield <BR>and method selection for "useful" simulations.<BR><BR>1)
 The Industrial Fluid Properties Simulation Collective (of which I am a <BR>member)http://fluidproperties.org/<BR><BR>2) The BioSimGrid, http://www.biosimgrid.org/<BR><BR>3) The protein folding challenges: http://predictioncenter.org/<BR><BR>4) If you are looking at something that is a crystal, see the Crystal <BR>Structure Prediction challenges: <BR>http://scripts.iucr.org/cgi-bin/paper?S0108768105016563<BR><BR>You could encourage every "modeling expert" you meet (particularly in <BR>academia) to support these efforts. The problems you are facing in trying to <BR>select a forcefield and method to use for your work are shared by everyone <BR>attempting to apply these methods. It is of benefit to us all that more <BR>validation/verification/guidence becomes available so that molecular <BR>simulations methods become "useful" to the wider world, and particularly in <BR>industry.<BR><BR><BR>Fiona Case<BR><BR><BR>----Original Message Follows----<BR>&gt; From: "Carlos Nunez
 carlos_javierna*o*yahoo.com" <OWNER-CHEMISTRY a\ccl.net><BR>Reply-To: "CCL Subscribers" <CHEMISTRY a\ccl.net><BR>To: "Case, Fiona " <FHCASE a\hotmail.com><BR>Subject: CCL: A review of force fields<BR>Date: Thu, 16 Mar 2006 20:57:41 -0500<BR><BR>Sent to CCL by: "Carlos Nunez" [carlos_javierna{:}yahoo.com]<BR>Hi,<BR><BR>See this:<BR><BR>MacKerell A. D. Jr. 2004. Empirical force fields for biological<BR>macromolecules: overview and issues. J. Comput. Chem. 25: 1584-1604.<BR><BR><BR>Hasta la proxima vez,<BR>Carlos N.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt<BR><BR><BR<BR<BR<BR<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/cgi-bin/ccl/send_ccl_message<BR><BR<BR>http://www.ccl.net/chemistry/sub_unsub.shtml<BR><BR<BR><BR<BR<BR><BR<BR><BR<BR>http://www.ccl.net/spammers.txt<BR><BR<BR><BR<BR><BR><BR><BR></BLOCKQUOTE><BR>
--0-632566050-1142991121=:76758--


From owner-chemistry@ccl.net Tue Mar 21 21:48:00 2006
From: "Gustavo L.C. Moura gustavo###mercury.chem.pitt.edu" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: Radial Distribution Function of Lanthanides
Message-Id: <-31270-060321214520-21428-cRue/Spwt96EjQjN31wUyA,,server.ccl.net>
X-Original-From: "Gustavo L.C. Moura" <gustavo,+,mercury.chem.pitt.edu>
Date: Tue, 21 Mar 2006 21:45:19 -0500


Sent to CCL by: "Gustavo L.C. Moura" [gustavo^mercury.chem.pitt.edu]
Dear CCL Readers,
     for educational purposes I need to plot the radial distribution function of lanthanides for comparing the distribution of the f orbitals with the s, p and d filled orbitals. I am looking for the exponents of these orbitals for lanthanides. They don't need to be the best exponents possible but simply good enough for showing the relative distribution between the orbitals. Would also be interesting to have these exponents for the trivalent ions.
      Thank you very much in advance for your help.
      Sincerely yours,
                   Gustavo L.C. Moura
               gustavo() mercury.chem.pitt.edu


From owner-chemistry@ccl.net Tue Mar 21 22:22:00 2006
From: "Tianxiao Yang xiaoyang_guelph _ yahoo.com" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: root flipping problem for MCSCF with Gamess
Message-Id: <-31271-060321174120-3975-MAiZRh2NQ/tPh6HWgkHz8g .. server.ccl.net>
X-Original-From: "Tianxiao  Yang" <xiaoyang_guelph[A]yahoo.com>
Date: Tue, 21 Mar 2006 17:41:19 -0500


Sent to CCL by: "Tianxiao  Yang" [xiaoyang_guelph() yahoo.com]
Hello,

I am having the serious problem of root flip for excited states calculation with MCSCF. Does anyone have any good suggestions to improve the excited states calculation with GAMESS? Thank you very much.

Xiao Yang