From owner-chemistry@ccl.net Tue May 12 06:13:01 2009
From: "=?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= jgcj{=}fct.unl.pt" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: heavy atoms
Message-Id: <-39291-090512055609-26485-4X4PxMtV4LHfK0NH/45eaA ~ server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= <jgcj+*+fct.unl.pt>
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Date: Tue, 12 May 2009 10:04:42 +0100
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Sent to CCL by: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= [jgcj::fct.unl.pt]
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u can try using cxcalc from the command line. it comes with MarvinBeans from
ChemAxon.com.

G.


2009/5/11 amit dong dongamit123[-]gmail.com <owner-chemistry-*-ccl.net>

> Hi group!
>
> Is there any tool that can calculate the heavy atom count of compounds
> given a multi-mol2 file?
>
> Thanks
> AD
>

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<div>u can try using cxcalc from the command line. it comes with MarvinBean=
s from ChemAxon.com.</div>
<div>=A0</div>
<div>G.<br><br><br></div>
<div class=3D"gmail_quote">2009/5/11 amit dong dongamit123[-]<a href=3D"htt=
p://gmail.com">gmail.com</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-=
chemistry-*-ccl.net">owner-chemistry-*-ccl.net</a>&gt;</span><br>
<blockquote class=3D"gmail_quote" style=3D"PADDING-LEFT: 1ex; MARGIN: 0px 0=
px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi group!<br><br>Is there any to=
ol that can calculate the heavy atom count of compounds given a multi-mol2 =
file? <br>
<br>Thanks<br><font color=3D"#888888">AD<br></font></blockquote></div><br>

--001636c5b3ffab32ca0469b3623a--


From owner-chemistry@ccl.net Tue May 12 06:50:00 2009
From: "Tristan Youngs t.youngs-x-qub.ac.uk" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Software suggestion
Message-Id: <-39292-090512044619-19101-vdCRLacrEkMdB1pH0lgUHw.@.server.ccl.net>
X-Original-From: Tristan Youngs <t.youngs~!~qub.ac.uk>
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Date: Tue, 12 May 2009 09:05:34 +0100
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Sent to CCL by: Tristan Youngs [t.youngs ~~ qub.ac.uk]
I echo the points that Herbert makes.  They are by and large exactly the
same reasons why I started to write Aten in the first place.
It was built with periodic systems (e.g. crystals, liquids) in mind, and
with a little effort you can add in support for export (and import) of
your own coordinates formats quite easily.

The homepage is http://www.projectaten.net.  Bear in mind that the
latest release available there is the 1.1 beta, but this will very soon
(in a week or so) be superseded by the vastly improved 1.2.

Cheers,
Tris.

Herbert Fruchtl herbert.fruchtl**st-andrews.ac.uk wrote:
> Sent to CCL by: Herbert Fruchtl [herbert.fruchtl-*-st-andrews.ac.uk]
> For molecules, there are more builders (or programs that contain a builder) than
> you can shake a stick at: Molden, ECCE, Maestro (free for academics), Arguslab,
> to name a few free ones.
>
> For periodic systems, it's not so rosy. I generally use gdis
> (http://gdis.sourceforge.net/). I wouldn't use it to build a complicated
> structure from scratch, but you can add atoms by a mouseclick and drag them
> around on the screen, create a supercell, cleave a surface by specifying the
> Miller indices, etc.
>
> More powerful, but with a steep learning curve (which I haven't yet found the
> energy to master) due to the lack of a GUI is tetr
> (http://www.cmmp.ucl.ac.uk/~lev/codes/lev00/).
>
> A commercial product I haven't used, and don't know the price of, is
> Crystalmaker (http://www.crystalmaker.com/).
>
> You are right about Materials Studio. It's the best, but their "academic
> pricing" is based on the wrong meaning of "academic" :-).
>
> What doesn't improve things is that each of them supports a few file formats,
> but it's always the wrong ones, and Babel isn't that good at periodic
> structures either (no VASP, no SIESTA, no CASTEP).
>
> HTH,
>
>   Herbert
>
> Quoting "Ugur Mart ugurmart ~~ yahoo.com" <owner-chemistry-.-ccl.net>:
>
>   
>> Can anyone suggest, if available, preferably free software for drawing
>> atomistic models, molecules and building crystal structures and surfaces.
>> Material Studio is I know one of the best but too expensive, isn't it?
>> Best regards
>> Ugur
>>
>>
>>
>>
>>     
>
>
>   

-- 
Dr. T. Youngs  (t.youngs###qub.ac.uk)
Atomistic Simulation Centre
Old Physics Building
Queen's University Belfast
Belfast, BT7 1NN, N.I.


From owner-chemistry@ccl.net Tue May 12 08:55:00 2009
From: "Alberto Pasamontes alberto.pasamontes:+:gmail.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Scaffold-Hopping software
Message-Id: <-39293-090512073153-14622-Ts7fJkuPpuvMN/5OmZw3qw|server.ccl.net>
X-Original-From: "Alberto  Pasamontes" <alberto.pasamontes|,|gmail.com>
Date: Tue, 12 May 2009 07:31:49 -0400


Sent to CCL by: "Alberto  Pasamontes" [alberto.pasamontes#,#gmail.com]
Dear,

We are planning a Scaffold-Hopping step (ligand based) in a virtual screening procedure. We know about LASSO and CODESSA. Any others suggestions about which software could we use to calculate descriptors and make a statistical analysis? 

thanks in advance


From owner-chemistry@ccl.net Tue May 12 09:29:00 2009
From: "M shabbir agri_chemist(!)yahoo.com" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL:G: PCM with bigger systems
Message-Id: <-39294-090512031337-9163-B4jnB1a3r92AZNFFflyiRw(a)server.ccl.net>
X-Original-From: "M  shabbir" <agri_chemist]*[yahoo.com>
Date: Tue, 12 May 2009 03:13:33 -0400


Sent to CCL by: "M  shabbir" [agri_chemist#yahoo.com]

Hello CCL colleagues,
Dear friends, finding not any solution of my problem I returned to my old teacher i.e. CCL. 
> From many days I am trying to run a single point PCM calculation (polarizability calculation with THF) on an organic molecule with 105 atoms in it. I have used a machine with 4 shared processors and 1024Mb memory but every time its gives error and job has been killed. I am guessing that error is due to the bigger size of the molecule so my question is;

Is there any keyword or parameter change that can complete this job?

Any other salvation method except Onsagar that can be easily used for bigger systems as in my case?

Output is looks as at the end
********************************************************************
Polarizable Continuum Model (PCM)
 =================================
 Model                : PCM.
 Atomic radii         : UA0 (Simple United Atom Topological Model).
 Polarization charges : Total charges.
 Charge compensation  : None.
 Solution method      : Matrix inversion.
 Cavity               : GePol (RMin=0.200 OFac=0.890).
                        Default sphere list used, NSphG=   59.
                        Tesserae with average area of 0.200 Ang**2.
 Solvent              : THF, Eps     =   7.580000
                               Eps(inf)=   1.971000
                               RSolv   =   2.560000 Ang.
 ------------------------------------------------------------------------------
 GePol: Number of tesserae being generated         =    8648
 GePol: Average area of tesserae                   =       0.10 Ang**2
 GePol: Minimum area of tessera                    =   0.10D-02 Ang**2
 GePol: Maximum area of tessera                    =    0.31621 Ang**2
 GePol: Number of small tesserae                   =       4
 GePol: Fraction of small tesserae (<1% of avg)    =       0.05%
 GePol: Total count of vertices                    =   31855
 GePol: Maximum number of vertices in a tessera    =       8
 GePol: Cavity surface area                        =    887.442 Ang**2
 GePol: Cavity volume                              =   1073.668 Ang**3
 Leave Link  301 at Sun May 10 14:45:59 2009, MaxMem=  134217728 cpu:     340.2
 (Enter /home/user4018/gaussian//g03/l302.exe)
 NPDir=0 NMtPBC=     1 NCelOv=     1 NCel=       1 NClECP=     1 NCelD=      1
         NCelK=      1 NCelE2=     1 NClLst=     1 CellRange=     0.0.
 One-electron integrals computed using PRISM.
 NBasis=   977 RedAO= T  NBF=   977
 NBsUse=   977 1.00D-06 NBFU=   977
 Precomputing XC quadrature grid using
 IXCGrd= 2 IRadAn=           0 IRanWt=          -1 IRanGd=           0.
 NRdTot=    7036 NPtTot=      905192 NUsed=      937065 NTot=      937081
 NSgBfM=   496   496   496   496.
 Leave Link  302 at Sun May 10 14:46:56 2009, MaxMem=  134217728 cpu:      48.7
 (Enter /home/user4018/gaussian//g03/l303.exe)
 DipDrv:  MaxL=1.
 Leave Link  303 at Sun May 10 14:46:59 2009, MaxMem=  134217728 cpu:       2.7
 (Enter /home/user4018/gaussian//g03/l401.exe)
 SCF N**3 symmetry information disabled.
 Harris functional with IExCor=  402 diagonalized for initial guess.
 ExpMin= 1.61D-01 ExpMax= 5.48D+03 ExpMxC= 8.25D+02 IAcc=1 IRadAn=         1 AccDes= 1.00D-06
 HarFok:  IExCor= 402 AccDes= 1.00D-06 IRadAn=         1 IDoV=1
 ScaDFX=  1.000000  1.000000  1.000000  1.000000
 Harris En= -2434.52809746882    
 Leave Link  401 at Sun May 10 14:47:21 2009, MaxMem=  134217728 cpu:      67.1
 (Enter /home/user4018/gaussian//g03/l502.exe)
 Closed shell SCF:
 Requested convergence on RMS density matrix=1.00D-08 within 128 cycles.
 Requested convergence on MAX density matrix=1.00D-06.
 Requested convergence on             energy=1.00D-06.
 No special actions if energy rises.
 Using DIIS extrapolation, IDIIS=  1040.
 Two-electron integral symmetry not used.
       937064 words used for storage of precomputed grid.
 IEnd=   4066500 IEndB=   4066500 NGot= 134217728 MDV= 131123375
 LenX= 131123375
 Fock matrices will be formed incrementally for  20 cycles.

 Cycle   1  Pass 1  IDiag  1:
 FoFCou: FMM=T IPFlag=           0 FMFlag=      100000 FMFlg1=        8193
 NFxFlg=           0 DoJE=F BraDBF=F KetDBF=F FulRan=T.
 Symmetry not used in FoFCou.
 FMM levels:  10  Number of levels for PrismC:   9
 PrismC:  NFx=      2048 NFxT=        20 NFxU=        20.
 PrismC:  NFx=      2048 NFxT=        20 NFxU=        20.
 PrismC:  NFx=      2048 NFxT=        20 NFxU=        20.
 PrismC:  NFx=      2048 NFxT=        20 NFxU=        20.


Regards
M.Shabbir


From owner-chemistry@ccl.net Tue May 12 10:19:01 2009
From: "Carsten Detering detering]*[biosolveit.de" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: Scaffold-Hopping software
Message-Id: <-39295-090512101729-4449-ACmfJyx2cosa2xrBDjPePw]-[server.ccl.net>
X-Original-From: "Carsten  Detering" <detering]|[biosolveit.de>
Date: Tue, 12 May 2009 10:17:25 -0400


Sent to CCL by: "Carsten  Detering" [detering:_:biosolveit.de]
Hi Alberto,

you can use FTrees for this. 
It calculates the similarity of two molecules by aligning them to each other 
(and this very fast: 0.5 Mio compounds ~ 1 minute), and is orthogonal to 
pretty much any other descriptor. 

To read more about the software, please look here:

www.biosolveit.com/ftrees


Cheers,
Carsten


__________________________________________________________________
Dr. Carsten Detering; Appl. Scientist      detering,,biosolveit.com
Phone EU: +49-2241-2525-0 / Fax: -525           www.biosolveit.com
Phone US: +1-617-297-2770
BioSolveIT GmbH - An der Ziegelei 79 - 53757 St.Augustin - Germany
Geschftsfhrer Dr. Christian Lemmen Amtsgericht Siegburg HRB 6261

Sent to CCL by: "Alberto  Pasamontes" [alberto.pasamontes#,#gmail.com]
Dear,

We are planning a Scaffold-Hopping step (ligand based) in a virtual screening 
procedure. We know about LASSO and CODESSA. Any others suggestions about 
which >software could we use to calculate descriptors and make a statistical 
analysis? 

thanks in advance


From owner-chemistry@ccl.net Tue May 12 10:53:01 2009
From: "mohamed aish mhmdaish]_[yahoo.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Fitted Coefficient for Ex and Ec Parts Only
Message-Id: <-39296-090512103423-16998-WwT77FUxWHB/MUd4IDudjg---server.ccl.net>
X-Original-From: mohamed aish <mhmdaish**yahoo.com>
Content-Type: multipart/alternative; boundary="0-1730561358-1242138852=:38937"
Date: Tue, 12 May 2009 07:34:12 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: mohamed aish [mhmdaish a yahoo.com]

--0-1730561358-1242138852=:38937
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

Hi Group;=0AMy question is about how the=0Acoefficients are calculated to c=
orrect the exchange and correlation energies. I=0Aknow that the coefficient=
s based on fitting to the one of the Thermochemical=0Adata; i.e. heats of f=
ormation, atomization energy, electron affinity, proton=0Aaffinity and so o=
n, and we know that the total energy, for example, for DFT is:=0AE(total) =
=3D ENN + ENE + EKE + EJ + Ex + Ec=0AWhere; ENN: nuclear=0Anuclear repulsio=
n=0AENE: nuclear electron =0AEKE: kinetic energy=0AEJ: electron-electron=0A=
repulsion=0AEx: exchange energy=0AEc: correlation energy=0ANow my question =
is: how the=0Afitted coefficients are calculated for Ex and Ec parts=0Aonly=
 without ENN, ENE, EKE and EJ?=0AIn other words: are the fitted coefficient=
s for the Ex and Ec calculated alone?=0A =0AThanx=0A=0A=0A      
--0-1730561358-1242138852=:38937
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:'times new roman', 'new york', times, se=
rif;font-size:14pt"><div></div><div style=3D"font-family:times new roman, n=
ew york, times, serif;font-size:14pt"><div style=3D"font-family:times new r=
oman, new york, times, serif;font-size:12pt"><div style=3D"font-family:'tim=
es new roman', 'new york', times, serif;font-size:14pt;"><div><p class=3D"M=
soNormal" style=3D"text-align:justify;">Hi Group;</p>=0A=0A<p class=3D"MsoN=
ormal" style=3D"text-align:justify;">My question is about how the=0Acoeffic=
ients are calculated to correct the exchange and correlation energies. I=0A=
know that the coefficients based on fitting to the one of the Thermochemica=
l=0Adata; i.e. heats of formation, atomization energy, electron affinity, p=
roton=0Aaffinity and so on, and we know that the total energy, for example,=
 for DFT is:</p>=0A=0A<p class=3D"MsoNormal" align=3D"center" style=3D"text=
-align:center;">E(total) =3D E<sub>NN</sub>=0A+ E<sub>NE </sub>+ E<sub>KE <=
/sub>+ E<sub>J </sub>+ E<sub>x </sub>+ E<sub>c</sub></p>=0A=0A<p class=3D"M=
soNormal" style=3D"text-align:justify;">Where; E<sub>NN</sub>: nuclear=0Anu=
clear repulsion</p>=0A=0A<p class=3D"MsoNormal" style=3D"text-align:justify=
;">E<sub>NE</sub>: nuclear electron </p>=0A=0A<p class=3D"MsoNormal" style=
=3D"text-align:justify;">E<sub>KE</sub>: kinetic energy</p>=0A=0A<p class=
=3D"MsoNormal" style=3D"text-align:justify;">E<sub>J</sub>: electron-electr=
on=0Arepulsion</p>=0A=0A<p class=3D"MsoNormal" style=3D"text-align:justify;=
">E<sub>x</sub>: exchange energy</p>=0A=0A<p class=3D"MsoNormal" style=3D"t=
ext-align:justify;">E<sub>c</sub>: correlation energy</p>=0A=0A<p class=3D"=
MsoNormal" style=3D"text-align:justify;">Now my question is: how the=0Afitt=
ed coefficients are calculated for E<sub>x</sub> and E<sub>c</sub> parts=0A=
only without E<sub>NN</sub>, E<sub>NE,</sub> E<sub>KE </sub>and E<sub>J</su=
b>?=0AIn other words: are the fitted coefficients for the E<sub>x</sub> and=
 E<sub>c</sub>=0Acalculated alone?</p>=0A=0A<p class=3D"MsoNormal" style=3D=
"text-align:justify;"> =A0</p> =0A=0A<p class=3D"MsoNormal" style=3D"text-a=
lign:justify;">Thanx</p>=0A=0A=0A=0A=0A</div><div style=3D"font-family:time=
s new roman, new york, times, serif;font-size:14pt;"><div style=3D"font-fam=
ily:arial, helvetica, sans-serif;font-size:13px;"><br></div></div><div styl=
e=3D""></div></div><br>=0A=0A      </div></div><div style=3D"position:fixed=
"></div></div><br>=0A=0A      </body></html>
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From owner-chemistry@ccl.net Tue May 12 11:29:01 2009
From: "Conley, Michael mconley_._leadscope.com" <owner-chemistry~!~server.ccl.net>
To: CCL
Subject: CCL: Scaffold-Hopping software
Message-Id: <-39297-090512112058-22697-3bMyOfKH7ok6n7Bjyh5K8g~!~server.ccl.net>
X-Original-From: "Conley, Michael" <mconley],[leadscope.com>
content-class: urn:content-classes:message
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	charset="us-ascii"
Date: Tue, 12 May 2009 10:48:15 -0400
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Sent to CCL by: "Conley, Michael" [mconley++leadscope.com]
Leadscope calculates a fingerprint of 27,000 pre-defined structural
features, on-the-fly predictive scaffolds, and nine properties (such as
aLogP, polar surface areas). The Leadscope software provides tools for
both statistic modeling as well as correlation of structural features
with biological endpoints.

You can obtain further information at www.leadscope.com or
info%leadscope.com.=20

Michael Conley
Leadscope, Inc.
1393 Dublin Road
Columbus, Ohio  43215
614-675-3768
614-675-3732 fax
www.leadscope.com


-----Original Message-----
> From: owner-chemistry+mconley=3D=3Dleadscope.com%ccl.net
[mailto:owner-chemistry+mconley=3D=3Dleadscope.com%ccl.net] On Behalf Of
Alberto Pasamontes alberto.pasamontes:+:gmail.com
Sent: Tuesday, May 12, 2009 7:32 AM
To: Conley, Michael
Subject: CCL: Scaffold-Hopping software


Sent to CCL by: "Alberto  Pasamontes" [alberto.pasamontes#,#gmail.com]
Dear,

We are planning a Scaffold-Hopping step (ligand based) in a virtual
screening procedure. We know about LASSO and CODESSA. Any others
suggestions about which software could we use to calculate descriptors
and make a statistical analysis?=20

thanks in advance



-=3D This is automatically added to each message by the mailing script =
=3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Tue May 12 12:44:00 2009
From: "Zsolt Bikadi zsolt.bikadi * virtuadrug.com" <owner-chemistry[-]server.ccl.net>
To: CCL
Subject: CCL: free docking
Message-Id: <-39298-090512124109-8879-GdSaKIKxV14bemziIfyCTA[-]server.ccl.net>
X-Original-From: "Zsolt Bikadi" <zsolt.bikadi~~virtuadrug.com>
Content-Type: multipart/alternative;
	boundary="----=_NextPart_000_007A_01C9D331.2FC3F740"
Date: Tue, 12 May 2009 18:40:56 +0200
MIME-Version: 1.0


Sent to CCL by: "Zsolt Bikadi" [zsolt.bikadi:-:virtuadrug.com]
This is a multi-part message in MIME format.

------=_NextPart_000_007A_01C9D331.2FC3F740
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	charset="iso-8859-1"
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Dear Jacopo,

you can try DockingServer (http://www.dockingserver.com) free, which is =
based on Autodock, but combined with quantum chemical methods by MOPAC =
and also uses more reliable ligand protonation methods, which greatly =
increase the accuracy of docking calculations.

Sincerely,
Zsolt Bikadi, PhD
DockingServer Team=20
  ----- Original Message -----=20
  From: Jacopo Sgrignani sgrigna]|[gmail.com=20
  To: Bikadi, Zsolt =20
  Sent: Friday, May 08, 2009 16:33 PM
  Subject: CCL: free docking


  Dear all
  can anybody suggest me a free (for academics) docking software. I'm =
using autodock but=20
  i have problem of docking accuracy on the system i'm studying.
  I would like to try another software, if possible with a GUI to setup =
the calculation.

  Thanks in advance

  Jacopo=20

------=_NextPart_000_007A_01C9D331.2FC3F740
Content-Type: text/html;
	charset="iso-8859-1"
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<HTML><HEAD>
<META http-equiv=3DContent-Type content=3D"text/html; =
charset=3Diso-8859-1">
<META content=3D"MSHTML 6.00.6000.21015" name=3DGENERATOR>
<STYLE></STYLE>
</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial size=3D2>Dear Jacopo,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>you can try DockingServer (<A=20
href=3D"http://www.dockingserver.com">http://www.dockingserver.com</A>) =
free,=20
which is based on Autodock, but combined with quantum chemical methods =
by MOPAC=20
and also uses&nbsp;more reliable ligand protonation methods, which =
greatly=20
increase the accuracy of docking calculations.</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV><FONT face=3DArial size=3D2>Sincerely,</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Zsolt Bikadi, PhD</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>DockingServer Team</FONT>&nbsp;</DIV>
<BLOCKQUOTE=20
style=3D"PADDING-RIGHT: 0px; PADDING-LEFT: 5px; MARGIN-LEFT: 5px; =
BORDER-LEFT: #000000 2px solid; MARGIN-RIGHT: 0px">
  <DIV style=3D"FONT: 10pt arial">----- Original Message ----- </DIV>
  <DIV=20
  style=3D"BACKGROUND: #e4e4e4; FONT: 10pt arial; font-color: =
black"><B>From:</B>=20
  <A title=3Downer-chemistry!A!ccl.net =
href=3D"mailto:owner-chemistry!A!ccl.net">Jacopo=20
  Sgrignani sgrigna]|[gmail.com</A> </DIV>
  <DIV style=3D"FONT: 10pt arial"><B>To:</B> <A =
title=3Dzsolt.bikadi!A!virtuadrug.com=20
  href=3D"mailto:zsolt.bikadi!A!virtuadrug.com">Bikadi, Zsolt </A> =
</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Sent:</B> Friday, May 08, 2009 =
16:33 PM</DIV>
  <DIV style=3D"FONT: 10pt arial"><B>Subject:</B> CCL: free =
docking</DIV>
  <DIV><BR></DIV>Dear all<BR>can anybody suggest me a free (for =
academics)=20
  docking software. I'm using autodock but <BR>i have problem of docking =

  accuracy on the system i'm studying.<BR>I would like to try another =
software,=20
  if possible with a GUI to setup the calculation.<BR><BR>Thanks in=20
  advance<BR><BR>Jacopo <BR></BLOCKQUOTE></BODY></HTML>

------=_NextPart_000_007A_01C9D331.2FC3F740--


From owner-chemistry@ccl.net Tue May 12 16:28:00 2009
From: "yvonnecmartin---comcast.net" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: Scaffold-Hopping software
Message-Id: <-39299-090512124226-9074-hx4LfQuH6hy8o2OB5JKhww]=[server.ccl.net>
X-Original-From: yvonnecmartin#comcast.net
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Content-Type: text/plain; charset=utf-8
Date: Tue, 12 May 2009 16:09:41 +0000 (UTC)
MIME-Version: 1.0


Sent to CCL by: yvonnecmartin[]comcast.net


Hi Alberto,=20



We recently compared a number of software programs in a publication for QSA=
R and Combinatorial Chemistry.=20

The abstract:

Beyond QSAR: Lead Hopping to Different Structures=20
Yvonne C. Martin and Steven Muchmore=20
Global Pharmaceutical Research and Development, Department R46Y=20
Abbott Laboratories, Abbott Park IL 60064 USA=20

We investigated the ability of several computer programs to detect lead hop=
s that had been reported to result from pharmacophore searching. None of th=
e methods identified all of these lead hops and some were not found by any =
program. The methods that performed the best identified different lead hops=
. Hence, we have deployed a lead hopping application that uses belief theor=
y to combine the results of ROCS, Daylight, and ECFP_6 similarities.=20



A list of the programs considered:=20

Daylight version=C2=A04.91 fingerprints of paths to length 7 hashed to 2048=
 bits; SciTegic version=C2=A06.1 ECFP_2, ECFP_4, and ECFP_6 and ECFC_2, ECF=
C_4, and ECFPC_6 fingerprints of paths and branches to the indicated length=
, both presence/absence and counts respectively, each hashed to 1024 bits; =
and ISIS keys calculated with PipelinePilot version=C2=A06.1, presence/abse=
nce of predefined substructures. OntoChem TOTO topological torsions version=
=C2=A01.0 using the MAPH atom-based method in which each atom of a topologi=
cal torsion is described by atom type, charge, pi electrons, attached hydro=
gens; SciTegic FCFP fingerprints analogous to the ECFP circular fingerprint=
s; BioSolveIT Feature trees version=C2=A01.5.1; and all eight types of Mole=
cular Networks 2D Adriana =C2=A0 version=C2=A02 autocorrelation vectors of =
length 10. In addition, we also examined the concatenated sigma , pi , and =
lone pair energy Adriana autocorrelation functions. Also Adriana descriptor=
s version 2 descriptors calculated from one Corina 3D conformer per molecul=
e. This includes eight types of 3D Adriana autocorrelation vectors encoded =
in 1=C2=A0=C3=85 increments from 2=C2=A0=E2=80=93=C2=A016=C2=A0=C3=85; the =
corresponding eight types of radial distribution function encoded in 16 int=
ervals from 1=C2=A0=E2=80=93=C2=A016=C2=A0=C3=85; and three types of surfac=
e autocorrelation function encoded in 24 intervals from 0.1 to 12=C3=85 wit=
h a point density of 5 per =C3=85 2 . Lastly, the fourth category considere=
d many 3D conformers; OpenEye ROCS and pharmacophore triplets programmed in=
-house. =C2=A0 We generated three-dimensional structures using OMEGA Versio=
n 2.0. For the query molecule (the molecule that is being matched) we calcu=
lated up to 10 conformers and for the database (the molecules that are bein=
g searched) up to 400 conformers per molecule were generated. We generated =
the pharmacophore triplet bit strings from the Omega conformers using an ap=
proach similar to that used to generate the Unity 3D distance bit strings.=
=20

Yvonne Martin

----- Original Message -----=20
> From: "Alberto Pasamontes alberto.pasamontes:+:gmail.com" <owner-chemistry()=
ccl.net>=20
To: "Yvonne  Martin" <yvonnecmartin()comcast.net>=20
Sent: Tuesday, May 12, 2009 6:31:49 AM GMT -06:00 US/Canada Central=20
Subject: CCL: Scaffold-Hopping software=20


Sent to CCL by: "Alberto =C2=A0Pasamontes" [alberto.pasamontes#,#gmail.com]=
=20
Dear,=20

We are planning a Scaffold-Hopping step (ligand based) in a virtual screeni=
ng procedure. We know about LASSO and CODESSA. Any others suggestions about=
 which software could we use to calculate descriptors and make a statistica=
l analysis?=20

thanks in advance=20



-=3D This is automatically added to each message by the mailing script =3D-=
=20=20=20=20=20
=C2=A0=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=
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Subscribe/Unsubscribe:=20
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Job: http://www.ccl.net/jobs=20=20=20=20
=C2=A0=C2=A0 =C2=A0 =C2=A0http://www.ccl.net/spammers.txt=20=20


From owner-chemistry@ccl.net Tue May 12 17:03:00 2009
From: "Orr Ravitz ravitz,simbiosys.ca" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: docking
Message-Id: <-39300-090512153533-22624-leDWIcBBsCxz1Ipre6cvIQ__server.ccl.net>
X-Original-From: "Orr  Ravitz" <ravitz::simbiosys.ca>
Date: Tue, 12 May 2009 15:35:29 -0400


Sent to CCL by: "Orr  Ravitz" [ravitz]_[simbiosys.ca]
Dear Gonalo and CCLers,

Yes, PS3 as in Sony's PlayStation 3. This gaming gadget is Cell B.E. based - a platform that is gradually becoming mainstream for scientific applications. PS3's are producing a good portion of the data for the folding at home project, and the cell processors power the Roadrunner super computer at Los Alamos.

The high performance of the cell is achieved via several factors:
- The multiple processor core consists of 1 hyperthreaded Power Processing Element (PPE) plus 8 Synergetic Processing Elements (SPE), each of them with its own DMA controller unit and local fast memory on-die.
- The SPEs are 128 bit vector processors with SIMD architecture using dual instruction pipes and are therefore capable of executing 8 floating point operations per clock cycle, each with 128x128bit registers and 256KB local store.

The parallelization, the vector operations and the unique memory configuration give the programmer a lot of flexibility in distributing tasks and data between the processors. Obviously you can't simply recompile your code for the PS3 and expect significant (or any) acceleration, but proper porting will get you tremendous speedup. You can find more technical information here:
http://www.simbiosys.ca/science/white_papers/eHiTS_on_the_Cell.pdf

The result of porting eHiTS to the cell is a 11X speedup for the lowest accuracy mode on average as measured using a set of over 6500 complexes. This study ran on a PS3 vs. an Intel Pentium 4 3.00GHz. A similar speed comparison for higher accuracy modes will be completed in the coming days. The results will be published as a technical note on SimBioSys' website:
http://www.simbiosys.ca/ehits/ehits_technical_notes.html

Best regards,
Orr


On May 8, 2009 02:18:11 pm Gonalo C. Justino jgcj[*]fct.unl.pt wrote:
> > One last facet---besides running on Intel platforms---you can also set up
> > a PS3 'farm' for low cost supercomputing performance. I am currently
> > doing this myself for high throughput metabolism predictions. So for
> > $400.00  I have a platform that will replace 8-30 nodes on a
> > cluster---and running the PS3's in parallel gives nearly linear scaling.
> >
> > Sorry, I'm... perplex...
>
> PS3 as in Playstation 3?! Really?!
>
> One PS3 = 8 - 30 nodes?
>
> Where's the how-to?
>
> Gonalo



-- 
Orr Ravitz, Ph.D.
SimBioSys Inc.
http://www.simbiosys.ca/
Tel: 1-416-741-4263


From owner-chemistry@ccl.net Tue May 12 18:15:01 2009
From: "NADIA BOUTABBA n_boutabba|-|yahoo.fr" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL:G: End of Minotr Frequency
Message-Id: <-39301-090512181303-5812-FA0b0RqRbeMADKOVT1Kp7w_+_server.ccl.net>
X-Original-From: "NADIA  BOUTABBA" <n_boutabba,,yahoo.fr>
Date: Tue, 12 May 2009 18:12:59 -0400


Sent to CCL by: "NADIA  BOUTABBA" [n_boutabba]![yahoo.fr]
Dear all,
I am studying weak chemical bond with dft. 
 the optimization is terminated successfully but 
in my log file  there is this message 
" End of Minotr Frequency-dependent properties file
   721 does not exist".i used geom=check guess =read
 to optimize in (3-21G,6-31G,6-31G*,6-31+G*,6-31++G**)
 the optimization terminated by "Normal termination of gaussian"
 but still including " End of Minotr Frequency-dependent 
properties file   721 does not exist".when i try to optimize*
 in 6-311++G** i have the error no lower point found. 
ccl memberes'message said that this is a problem of memory ,
 please how to solve it?here is my file.com
%Nproc=8
%mem=200MW
%Chk=trife
%save
%rwf=r1,240mw,r2,240mw,r3,240mw,r4,240mw,r5,240mw,r6,240mw,r7,240mw,r8,-1
# Bvwn5/3-21G IOp(5/45=10000200) IOp(5/46=07200800) IOp(5/47=00001000)
pop=none opt=calcall nosymm
 
fer
 
0,3
Fe
 C  1   cfe2   
 c   1 cfe3       2 cfec3     
 o   2 oc4        1 ocfe4        3 dih4   
 o   3 oc5        2 occ5         1 dih5   
 c   1 cfe6       2 cfec6        3 dih6   
 o   6 oc7        1 ocfe7        3 dih7   
 

 cfe2=1.78686445
 cfe3=1.78692725
 cfec3=133.97875779
 oc4=1.17849842
 ocfe4=180.96729287
 dih4=-0.32103779
 oc5=1.17849536
 occ5=132.9476645
 dih5=-179.8686489
 cfe6=3.19044568
 cfec6=112.98717548
 dih6=180.0
 oc7=1.17840768
 ocfe7=0.01275558
 dih7=0.0


Nadia boutabba
3902,college station 1310
Texas,77801
tel +001-979-402-7688


From owner-chemistry@ccl.net Tue May 12 20:56:00 2009
From: "John McKelvey jmmckel||gmail.com" <owner-chemistry===server.ccl.net>
To: CCL
Subject: CCL: Generating symmetry from where it almost exists...
Message-Id: <-39302-090512205415-14548-SvKToa1BbSGTxsA/R4cw1g===server.ccl.net>
X-Original-From: John McKelvey <jmmckel{=}gmail.com>
Content-Type: multipart/alternative; boundary=001e680f18bce1ada70469c0a5ef
Date: Tue, 12 May 2009 20:54:04 -0400
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel::gmail.com]
--001e680f18bce1ada70469c0a5ef
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: 7bit

Folks,

I have a bunch of cartesian geometries that have "almost" C2 symmetry.
Graphical inspection says yhey should be C2 but the code I'm using won't
generate C2, even with large "out-of-symmetry" threshold values.  Can anyone
point me to a simple utility that could be used to clean these structures
up?

Thanks!

John McKelvey

--001e680f18bce1ada70469c0a5ef
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Folks,<br><br>I have a bunch of cartesian geometries that have &quot;almost=
&quot; C2 symmetry.=A0 Graphical inspection says yhey should be C2 but the =
code I&#39;m using won&#39;t generate C2, even with large &quot;out-of-symm=
etry&quot; threshold values.=A0 Can anyone point me to a simple utility tha=
t could be used to clean these structures up?<br>
<br>Thanks!<br><br>John McKelvey<br>

--001e680f18bce1ada70469c0a5ef--


From owner-chemistry@ccl.net Tue May 12 23:01:01 2009
From: "Kalju Kahn kalju-x-chem.ucsb.edu" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL: Generating symmetry from where it almost exists...
Message-Id: <-39303-090512221033-12835-obntMjDxgyNPr7KnCfY9UA=server.ccl.net>
X-Original-From: "Kalju Kahn" <kalju|chem.ucsb.edu>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Tue, 12 May 2009 19:10:17 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: "Kalju Kahn" [kalju*_*chem.ucsb.edu]
Hi John,

I like SYMMOL.  Also, there is a rudimentary python script that takes in
MDL MOL files and spits out symmetric structures and symmetry-unique atoms
in GAMESS-like XYZ format available at:

http://www.chem.ucsb.edu/~kalju/chem226/public/pcgamess_tutorial_A2.html

Let me know if you have any trouble,

Kalju

> Folks,
>
> I have a bunch of cartesian geometries that have "almost" C2 symmetry.
> Graphical inspection says yhey should be C2 but the code I'm using won't
> generate C2, even with large "out-of-symmetry" threshold values.  Can
> anyone
> point me to a simple utility that could be used to clean these structures
> up?
>
> Thanks!
>
> John McKelvey
>


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC Santa Barbara, CA 93106