From owner-chemistry@ccl.net Thu Aug  7 05:25:01 2008
From: "Vivek Sharma vivek.viv.sharma*gmail.com" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: Linux cluster for QM calculations
Message-Id: <-37497-080807052239-13417-NOFQBK0Aivs/ku4b4wfBPA~~server.ccl.net>
X-Original-From: "Vivek  Sharma" <vivek.viv.sharma-x-gmail.com>
Date: Thu, 7 Aug 2008 05:22:36 -0400


Sent to CCL by: "Vivek  Sharma" [vivek.viv.sharma-,-gmail.com]
Dear CCL people,

I have seen some emails on CCL; people asking about cluster/computer configurations for QM calculations, thus I also would like to know a bit. Actually, I would like to have a little feedback on the linux cluster we are building. We  because of lack of technical expertise, are keeping the things on low profile and would like to improve from there. The main idea is to have a separate cluster (which will be improved in due course of time) for QM calculations. We are starting with 2-node system:

a) 2.2 - 2.6GHz AMD Athlon per node.
b) 3GB RAM per node.
c) 160GB per node HDD.
d) Server Class Motherboard per node and possibly extra-slots for increasing
RAM and HDD capacity.
e) Good graphics card per node.
f) DVD ROM per node.
g) 2 Ethernet adaptors per node.
h) Misc: 1 Monitor, Cables, etc.

And, most probably we will be buying these machines of some BRAND (as we would like to have maintenance available in case of problems). And for OS also, we are thinking about RHEL 5 (with package for HPC) (again for maintenance reasons).

I apologise if details mentioned here are not-so-specific, but any input will be of great help. First question is that does this configuration sound decent, sure there is no-upper limit for QM calculations, but for starting purposes, does it look okay OR to say, where it seems utmost to improve, PROCESSORS or Memory (?). Secondly, how easy/difficult it is to further add-up the hardware, say nodes of different configuration from previous ones (?). Also, any little inputs regarding the possible programs, which can be parallelised easily over such a machine, will be helpful too.

Thanks very much in advance,


Vivek Sharma
vivek.viv.sharmaATgmail.com
IMM, India.


From owner-chemistry@ccl.net Thu Aug  7 07:29:00 2008
From: "Arun Venkatnathan arunv1973|a|yahoo.com" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37498-080807054744-23794-XYVgB2RjeYZeuKEuwYdl4g * server.ccl.net>
X-Original-From: Arun Venkatnathan <arunv1973(a)yahoo.com>
Content-Type: multipart/alternative; boundary="0-542571277-1218098851=:63033"
Date: Thu, 7 Aug 2008 01:47:31 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Arun Venkatnathan [arunv1973*o*yahoo.com]
--0-542571277-1218098851=:63033
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Dear All,

I am looking for a free computational Chemistry software(s) which works in =
Windows operating systems which can do simple ab initio calculations as wel=
l as molecular mechanics. This will be used primarily as a teaching tool fo=
r 2nd and 3rd year undergraduate students.=A0 Additionally, software which =
can display orbitals etc will also be useful as a teaching tool.=20

Any recommendations on choice of software for teaching or pointers towards =
any free software will be deeply appreciated.

Thanks,
Arun=20

Dr. Arun Venkatnathan
Assistant Professor, Chemistry
Indian Institute of Science Education and Research Pune
India. 411021=20
Tel: 91-20-2590-8044

=0A=0A=0A      
--0-542571277-1218098851=:63033
Content-Type: text/html; charset=us-ascii

<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;">Dear All,<br><br>I am looking for a free computational Chemistry software(s) which works in Windows operating systems which can do simple ab initio calculations as well as molecular mechanics. This will be used primarily as a teaching tool for 2nd and 3rd year undergraduate students.&nbsp; Additionally, software which can display orbitals etc will also be useful as a teaching tool. <br><br>Any recommendations on choice of software for teaching or pointers towards any free software will be deeply appreciated.<br><br>Thanks,<br>Arun <br><br>Dr. Arun Venkatnathan<br>Assistant Professor, Chemistry<br>Indian Institute of Science Education and Research Pune<br>India. 411021 <br>Tel: 91-20-2590-8044<br><br></td></tr></table><br>

      
--0-542571277-1218098851=:63033--


From owner-chemistry@ccl.net Thu Aug  7 09:33:01 2008
From: "Anatoli Korkin a_korkin__yahoo.com" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37499-080807093216-771-xQ7EbTtdeIdi7SQo6OFY8w-x-server.ccl.net>
X-Original-From: Anatoli Korkin <a_korkin*|*yahoo.com>
Content-Type: text/plain; charset=us-ascii
Date: Thu, 7 Aug 2008 06:32:04 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Anatoli Korkin [a_korkin_+_yahoo.com]
Check this if you wish:

http://asdn.net/asdn/links/software.shtml


--- On Thu, 8/7/08, Arun Venkatnathan arunv1973|a|yahoo.com <owner-chemistry[-]ccl.net> wrote:

> From: Arun Venkatnathan arunv1973|a|yahoo.com <owner-chemistry[-]ccl.net>
> Subject: CCL: Computational Chemistry software
> To: "Korkin, Anatoli " <a_korkin[-]yahoo.com>
> Date: Thursday, August 7, 2008, 1:47 AM
> Dear All,
> 
> I am looking for a free computational Chemistry software(s)
> which works in Windows operating systems which can do simple
> ab initio calculations as well as molecular mechanics. This
> will be used primarily as a teaching tool for 2nd and 3rd
> year undergraduate students.  Additionally, software which
> can display orbitals etc will also be useful as a teaching
> tool. 
> 
> Any recommendations on choice of software for teaching or
> pointers towards any free software will be deeply
> appreciated.
> 
> Thanks,
> Arun 
> 
> Dr. Arun Venkatnathan
> Assistant Professor, Chemistry
> Indian Institute of Science Education and Research Pune
> India. 411021 
> Tel: 91-20-2590-8044


From owner-chemistry@ccl.net Thu Aug  7 10:08:01 2008
From: "Igor Filippov Contr igorf(-)helix.nih.gov" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Linux cluster for QM calculations
Message-Id: <-37500-080807092924-499-3FGNnPUlwe5pwOlFssdnsQ]~[server.ccl.net>
X-Original-From: "Igor Filippov [Contr]" <igorf(-)helix.nih.gov>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Thu, 07 Aug 2008 08:31:22 -0400
Mime-Version: 1.0


Sent to CCL by: "Igor Filippov [Contr]" [igorf:helix.nih.gov]
Dear Vivek,


> a) 2.2 - 2.6GHz AMD Athlon per node.
I would suggest quad-core Intel Core 2 cpu's. You will get more cpu
horsepower at this point.
> b) 3GB RAM per node.
Definitely more RAM. Get a slower CPU if you have to, but 2Gb RAM per
core is what I would recommend. If you lack cpu power you will simply
have to wait longer for your computation to complete, if you don't have
enough RAM your computation may not run at all.

> c) 160GB per node HDD.
Same for the disk space. Not sure what kind of calculations you're
planning to run, but it's quite possible to run out of local disk.
750 Gb hdd's are the best price/capacity point at the moment I believe.

> d) Server Class Motherboard per node and possibly extra-slots for increasing
> RAM and HDD capacity.
Make sure it's compatible with Linux.

> e) Good graphics card per node.
What for? If it's a cluster node the graphics card is pretty much
useless.

> f) DVD ROM per node.
> g) 2 Ethernet adaptors per node.
> h) Misc: 1 Monitor, Cables, etc.
Hardware-wise I suggest you invest in good power supplies and CPU fans.
Regular stock cpu fans that some name brands put inside will not cut it
on a PC that runs heavy computations 24/7.

> 
> And, most probably we will be buying these machines of some BRAND (as we would like to have maintenance available in case of problems). And for OS also, we are thinking about RHEL 5 (with package for HPC) (again for maintenance reasons).
Oh, I would definitely not recommend buying a name brand. Personally I
prefer something that is built from components I can get at a local
store so that I can fix things myself. But your mileage may wary of
course.

As for the software I would point you to CentOS and OSCAR -
http://svn.oscar.openclustergroup.org/trac/oscar

with OSCAR you can add more nodes in minutes and it has popular TORQUE
batch system and a good set of other cluster tools.

Hope this helps,
Igor
> 
> I apologise if details mentioned here are not-so-specific, but any input will be of great help. First question is that does this configuration sound decent, sure there is no-upper limit for QM calculations, but for starting purposes, does it look okay OR to say, where it seems utmost to improve, PROCESSORS or Memory (?). Secondly, how easy/difficult it is to further add-up the hardware, say nodes of different configuration from previous ones (?). Also, any little inputs regarding the possible programs, which can be parallelised easily over such a machine, will be helpful too.
> 
> Thanks very much in advance,
> 
> 
> Vivek Sharma
> vivek.viv.sharmaATgmail.com
> IMM, India.> 
-- 
Igor Filippov [Contr] <igorf+*+helix.nih.gov>


From owner-chemistry@ccl.net Thu Aug  7 10:44:00 2008
From: "Mr shabbir shabbir*_*nenu.edu.cn" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL:G: Crysallographic structure Vs optimized
Message-Id: <-37501-080806075208-8167-sKFt/Hgs6iQYNm6ZnvScbw-#-server.ccl.net>
X-Original-From: "Mr  shabbir" <shabbir,nenu.edu.cn>
Date: Wed, 6 Aug 2008 07:52:02 -0400


Sent to CCL by: "Mr  shabbir" [shabbir__nenu.edu.cn]
Hello CCL users!
I am a in some confusion want to explain it. Please If some one have an idea let me know also.
I have taken a crystallographic structure and optimized it using Gaussian03 with C2 symmetry and b3lyp/6-31G* method. After optimization it gave me a round about planer structure. After this I have calculated its UV and IR spectra that is in good agreement with experimental values but the crystallographic structure has a dihedral angle 40 degree with side pyrrol rings which is not in my optimized structure. So can I say that my Gassphase optimized structure is reliable on the basis of calculated experimental values and start my futher calculations? Secondly I tried to freeze that dihedral angle using guessview but it could not freeze during optimization. How to freeze dihedral angle during optimization so that it will not change during calculations? 
 Mr.Shabbir
Northeast normal university Changchun
P.R.China
shabbir . nenu.edu.cn


From owner-chemistry@ccl.net Thu Aug  7 11:18:01 2008
From: "Andrew Dalke dalke\a/dalkescientific.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Python training for cheminformatics
Message-Id: <-37502-080806090108-26752-KdzIrYpOt9ShTJchp6vsRw(0)server.ccl.net>
X-Original-From: Andrew Dalke <dalke{}dalkescientific.com>
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Date: Wed, 6 Aug 2008 14:00:51 +0200
Mime-Version: 1.0 (Apple Message framework v753.1)


Sent to CCL by: Andrew Dalke [dalke.:.dalkescientific.com]
Hello all,

    I will be teaching a two-day training course in Python
programming in Leipzig, Germany on 6-7 October.  This course
is designed for cheminformatics researchers who want to be
more effective at the software side of their work.

    If you are interested in participating in the course,
please contact me.

    For more details see http://dalkescientific.com/training/ .

    I am also tentatively planning a course in the San Francisco
Bay Area in early December.


				Andrew
				dalke_+_dalkescientific.com


From owner-chemistry@ccl.net Thu Aug  7 11:53:01 2008
From: "=?utf-8?Q?_Jorge_Rodr=C3=ADguez_Becerra?= jorberr[*]ciq.uchile.cl" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site acive?
Message-Id: <-37503-080806020142-4322-TEXtMUhB7lpQDeisQ9yW0A__server.ccl.net>
X-Original-From: =?utf-8?Q?_Jorge_Rodr=C3=ADguez_Becerra?= <jorberr%ciq.uchile.cl>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=utf-8
Date: Wed, 6 Aug 2008 01:32:52 -0400 (CLT)
MIME-Version: 1.0


Sent to CCL by: =?utf-8?Q?_Jorge_Rodr=C3=ADguez_Becerra?= [jorberr%x%ciq.uchile.cl]
Hi, I have a system that present two ligand in the same active site (pi-stacking interactions between ligand). So, in the autodock 4 program I can`t use this dimer system becouse autodock recognizes only one ligand of the dimer (a connectivity problem). If someone can help me. Because I don't knwon, how I can dock two ligand at same site acive? 

I will greatly appreciate it if someone helps me

Jorge R


From owner-chemistry@ccl.net Thu Aug  7 12:28:01 2008
From: "Jorge Rodriguez jorberr]_[ciq.uchile.cl" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site active with autodock?
Message-Id: <-37504-080806013750-27753-aUHecUVBCKmAcWPfI1SXkg^_^server.ccl.net>
X-Original-From: "Jorge  Rodriguez" <jorberr=ciq.uchile.cl>
Date: Wed, 6 Aug 2008 01:37:46 -0400


Sent to CCL by: "Jorge  Rodriguez" [jorberr++ciq.uchile.cl]
Hi, I have a system that present two ligand in the same active site (pi-stacking interactions between ligand). So, in the autodock 4 program I can`t use this dimer system becouse autodock recognizes only one ligand of the dimer (a connectivity problem). If someone can help me. Because I don't konw, how I can dock two ligand at same site active?

I will greatly appreciate it if someone helps me


From owner-chemistry@ccl.net Thu Aug  7 13:03:02 2008
From: "Alcides Simao alsimao(0)gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37505-080807103904-8094-GYHusExZavBa6ZJ3UjxeaA^_^server.ccl.net>
X-Original-From: "Alcides Simao" <alsimao _ gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_13330_28831582.1218118171418"
Date: Thu, 7 Aug 2008 15:09:31 +0100
MIME-Version: 1.0


Sent to CCL by: "Alcides Simao" [alsimao*_*gmail.com]
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Hello Arun!

There are multiple software to choose from! But be CAREFUL with the licenses
:)

I personally recomend GAMESS!

http://www.msg.ameslab.gov/GAMESS/

GAMESS is fully featured on ab initio, semi-empiric and has the basis for MM
calculations

NWCHEM is another free, research-grade software, but it has a little more
restrictive license.

Another good package is ORCA

http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php

For DFT calculations, OCTOPUS ( http://www.tddft.org/ ) , as well as abinit
(http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066) are
good choices!

Zodiac and Vega ZZ are good programs for Cheminformatics and MM work :)
Tinker is also a good program!

http://homepage.mac.com/swain/Macinchem/page11/page11.html <- Zodiac
http://www.ddl.unimi.it/vega/index.htm <- Vega ZZ
http://dasher.wustl.edu/tinker/ <- Tinker

I hope this helps you :)

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<div dir="ltr">Hello Arun!<br><br>There are multiple software to choose from! But be CAREFUL with the licenses :)<br><br>I personally recomend GAMESS! <br><br><a href="http://www.msg.ameslab.gov/GAMESS/">http://www.msg.ameslab.gov/GAMESS/</a><br>
<br>GAMESS is fully featured on ab initio, semi-empiric and has the basis for MM calculations<br><br>NWCHEM is another free, research-grade software, but it has a little more restrictive license.<br><br>Another good package is ORCA<br>
<br><a href="http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php">http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php</a><br><br>For DFT calculations, OCTOPUS ( <a href="http://www.tddft.org/">http://www.tddft.org/</a> ) , as well as abinit (<a href="http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066">http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066</a>) are good choices!<br>
<br>Zodiac and Vega ZZ are good programs for Cheminformatics and MM work :) Tinker is also a good program!<br><br><a href="http://homepage.mac.com/swain/Macinchem/page11/page11.html">http://homepage.mac.com/swain/Macinchem/page11/page11.html</a> &lt;- Zodiac<br>
<a href="http://www.ddl.unimi.it/vega/index.htm">http://www.ddl.unimi.it/vega/index.htm</a> &lt;- Vega ZZ<br><a href="http://dasher.wustl.edu/tinker/">http://dasher.wustl.edu/tinker/</a> &lt;- Tinker<br><br>I hope this helps you :)<br>
</div>

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From owner-chemistry@ccl.net Thu Aug  7 13:39:01 2008
From: "Conley, Michael mconley#,#leadscope.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: FDA SAR-ready Carcinogenicity Database Now Available
Message-Id: <-37506-080807100822-17124-uKWEKcgoaIGbM1wTTtE1xw^_^server.ccl.net>
X-Original-From: "Conley, Michael" <mconley(!)leadscope.com>
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Date: Thu, 7 Aug 2008 09:35:23 -0400
MIME-Version: 1.0


Sent to CCL by: "Conley, Michael" [mconley:+:leadscope.com]
This is a multi-part message in MIME format.

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	charset="us-ascii"
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Columbus, Ohio August 1, 2008 - Leadscope announces the availability of
the FDA SAR-Ready Carcinogenicity Database. =20

=20

The FDA SAR-Ready Carcinogenicity database has been constructed by
Leadscope and the U.S. Food & Drug Administration (FDA) under their
Cooperative Research & Development Agreement.  This database contains
1,634 SAR structures with 9,557 test results, compiled from
non-proprietary FDA records and other sources.  Structures are provided
in the SAR, neutral and tested forms.

=20

All structures and test calls have been verified for accuracy while both
structures and data have been balanced to facilitate model training set
selection.  Toxicity endpoints include Rat Male, Rat Female, Mouse Male
and Mouse Female.

=20

Loftus Lucas, Leadscope's CEO, said, "The combination of SAR-ready data
and Leadscope's model building capability allows scientists to easily
build and apply transparent carcinogenicity models." =20

=20

To view a pre-recorded demonstration of the FDA SAR-Ready
Carcinogenicity database, visit
www.leadscope.com/sar_carcinogenicity_database/
<http://www.leadscope.com/sar_carcinogenicity_database/> .  For further
information on this new database or to request on-line demonstration
with a Leadscope scientist contact us at info|leadscope.com
<mailto:info|leadscope.com> .=20

=20

=20

Contact:

=20

Loftus Lucas

Leadscope, Inc.

1393 Dublin Road

Columbus, Ohio 43215

Phone: 614-340-1399

Fax:  614-675-3732

Email:  info|leadscope.com =20

=20


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<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
  12.0pt'>Columbus</span></font>, Ohio August 1, 2008 &#8211; Leadscope =
announces
the availability of the FDA SAR-Ready Carcinogenicity Database.&nbsp; =
</p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>The FDA SAR-Ready Carcinogenicity database has been constructed =
by
Leadscope and the U.S. Food &amp; Drug Administration (FDA) under their
Cooperative Research &amp; Development Agreement.&nbsp; This database =
contains 1,634
SAR structures with 9,557 test results, compiled from non-proprietary =
FDA
records and other sources.&nbsp; Structures are provided in the SAR, =
neutral and
tested forms.</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>All structures and test calls have been verified for accuracy =
while
both structures and data have been balanced to facilitate model training =
set
selection.&nbsp; Toxicity endpoints include Rat Male, Rat Female, Mouse =
Male and
Mouse Female.</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Loftus Lucas, Leadscope&#8217;s CEO, said, &#8220;The =
combination of
SAR-ready data and Leadscope&#8217;s model building capability allows
scientists to easily build and apply transparent carcinogenicity
models.&#8221;&nbsp; </span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>To view a pre-recorded demonstration of the FDA SAR-Ready =
Carcinogenicity
database, visit <a =
href=3D"http://www.leadscope.com/sar_carcinogenicity_database/"><span
style=3D'text-decoration:none'>www.leadscope.com/sar_carcinogenicity_data=
base/</span></a>.&nbsp;
For further information on this new database or to request on-line
demonstration with a Leadscope scientist contact us at <a
href=3D"mailto:info|leadscope.com"><span =
style=3D'text-decoration:none'>info|leadscope.com</span></a>.
</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Contact:</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>&nbsp;</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Loftus Lucas</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Leadscope, Inc.</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
  12.0pt'>1393 Dublin Road</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
  12.0pt'>Columbus</span></font>, Ohio 43215</p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Phone: 614-340-1399</span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
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<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>Email:&nbsp; info|leadscope.com&nbsp; </span></font></p>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
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From owner-chemistry@ccl.net Thu Aug  7 14:12:02 2008
From: "Sriraj Srinivasan ss537|,|drexel.edu" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37507-080807104435-12801-UP1pVvE8MvjmwdYTJ91/VQ---server.ccl.net>
X-Original-From: Sriraj Srinivasan <ss537*drexel.edu>
Content-Disposition: inline
Content-Language: en
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=iso-8859-1
Date: Thu, 07 Aug 2008 09:39:19 -0400
MIME-Version: 1.0


Sent to CCL by: Sriraj Srinivasan [ss537,,drexel.edu]
Hey Arun=2C


PC-GAMESS is a good option=2C which is free for download to use on Window=
s OS=2E You should also download Macmolplt - the graphical software to vi=
ew structures and orbitals=2E  Molekel is another free graphical software=
 that serves the same purpose=2E


Best Regards

Sriraj

----- Original Message -----
> From=3A =22Arun Venkatnathan arunv1973=7Ca=7Cyahoo=2Ecom=22 =3Cowner-chem=
istry=40ccl=2Enet=3E
Date=3A Thursday=2C August 7=2C 2008 4=3A47 am
Subject=3A CCL=3A Computational Chemistry software

=3E Dear All=2C
=3E =

=3E I am looking for a free computational Chemistry software(s) which =

=3E works in Windows operating systems which can do simple ab initio =

=3E calculations as well as molecular mechanics=2E This will be used =

=3E primarily as a teaching tool for 2nd and 3rd year undergraduate =

=3E students=2E=A0 Additionally=2C software which can display orbitals et=
c =

=3E will also be useful as a teaching tool=2E =

=3E =

=3E Any recommendations on choice of software for teaching or pointers =

=3E towards any free software will be deeply appreciated=2E
=3E =

=3E Thanks=2C
=3E Arun =

=3E =

=3E Dr=2E Arun Venkatnathan
=3E Assistant Professor=2C Chemistry
=3E Indian Institute of Science Education and Research Pune
=3E India=2E 411021 =

=3E Tel=3A 91-20-2590-8044
=3E =

=3E =

=3E =

=3E =

=3E


From owner-chemistry@ccl.net Thu Aug  7 14:49:02 2008
From: "Hemant Srivastava hemantkrsri%gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL:G: Crysallographic structure Vs optimized
Message-Id: <-37508-080807113018-30662-VnuubneqKp0u71cLiWQJbA^server.ccl.net>
X-Original-From: "Hemant Srivastava" <hemantkrsri-*-gmail.com>
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Date: Thu, 7 Aug 2008 18:30:02 +0300
MIME-Version: 1.0


Sent to CCL by: "Hemant Srivastava" [hemantkrsri+*+gmail.com]
Dear Shabbir,

For fixing diahedral angle you can write following in input file al last.
D 1 2 3 4 F
where 1 2 3 4 are atom numbers.

For the other problem you have I think you should try different
method/basis or solvent calculation.

Hope it will help.

Hemant Kumar Srivastava,
The Hebrew University of Jerusalem
===================================


On 8/6/08, Mr shabbir shabbir*_*nenu.edu.cn <owner-chemistry^^ccl.net> wrote:
>
>  Sent to CCL by: "Mr  shabbir" [shabbir__nenu.edu.cn]
>  Hello CCL users!
>  I am a in some confusion want to explain it. Please If some one have an idea let me know also.
>  I have taken a crystallographic structure and optimized it using Gaussian03 with C2 symmetry and b3lyp/6-31G* method. After optimization it gave me a round about planer structure. After this I have calculated its UV and IR spectra that is in good agreement with experimental values but the crystallographic structure has a dihedral angle 40 degree with side pyrrol rings which is not in my optimized structure. So can I say that my Gassphase optimized structure is reliable on the basis of calculated experimental values and start my futher calculations? Secondly I tried to freeze that dihedral angle using guessview but it could not freeze during optimization. How to freeze dihedral angle during optimization so that it will not change during calculations?
>   Mr.Shabbir
>  Northeast normal university Changchun
>  P.R.China
>  shabbir++nenu.edu.cn>
>
>


From owner-chemistry@ccl.net Thu Aug  7 15:23:00 2008
From: "Ol Ga eurisco1[*]pochta.ru" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37509-080807113653-3160-V8IESCM5nmz4IKvw9Qi3Bw|server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1^_^pochta.ru>
Date: Thu, 7 Aug 2008 11:36:49 -0400


Sent to CCL by: "Ol  Ga" [eurisco1..pochta.ru]
Dear Dr. Arun Venkatnathan,

I suggest you to use for your aims

1)	the program WinGAMESS (GAMESS US) with Tinker for QC and MM calculations with programs Avogadro (additional and very important features are input file generation and MM calculations internally executing), wxMacMolPlot, gMolden for geometry generation and visualization steps of optimization, orbitals etc.

2)	the program ORCA for QC calculation with gMolden, wxMacMolPlot (on .trj-file) as well as Molekel, gOpenMol. The program ORCA is an excellent and robust tool for  QC calculations.  

It will be necessary to generate sometimes .cub and .fch-files for  visualization  of orbitals etc.


Sincerely,

Ol Ga


PS I use this programs and in this (_1_ and _2_) combinations. 


----- Original Message ----- 
>From: Arun Venkatnathan arunv1973|a|yahoo.com 
>To: Ga, Ol  
>Sent: Thursday, August 07, 2008 12:47 PM
>Subject: CCL: Computational Chemistry software


>Dear All,

>I am looking for a free computational Chemistry software(s) which works in >Windows operating systems which can do simple ab initio calculations as >well as molecular mechanics. This will be used primarily as a teaching >tool for 2nd and 3rd year undergraduate students.  Additionally, software >which can display orbitals etc will also be useful as a teaching tool. 

>Any recommendations on choice of software for teaching or pointers towards >any free software will be deeply appreciated.

>Thanks,
>Arun


From owner-chemistry@ccl.net Thu Aug  7 15:58:01 2008
From: "Abdul Hameed, MohamedDiwanMo mabdu3!^!email.uky.edu" <owner-chemistry-x-server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site acive?
Message-Id: <-37510-080807132738-26253-ofJpuvyGrxbJnMT9VgMt2A-x-server.ccl.net>
X-Original-From: "Abdul Hameed, MohamedDiwanMo" <mabdu3 * email.uky.edu>
Content-Language: en-US
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	boundary="_000_62D3F106CB16C34D825A1B75EFBA683901697724CDEX7FM04adukye_"
Date: Thu, 7 Aug 2008 12:31:32 -0400
MIME-Version: 1.0


Sent to CCL by: "Abdul Hameed, MohamedDiwanMo" [mabdu3#,#email.uky.edu]
--_000_62D3F106CB16C34D825A1B75EFBA683901697724CDEX7FM04adukye_
Content-Type: text/plain; charset="us-ascii"
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Hi,

If you know how the two ligands bind, then you can divide the active site a=
nd do two separate docking. i.e., (in case of autodock) you can define the =
grid such that it covers one part of the active site and dock the ligand. S=
imilarly you can dock the second ligand to the other half of active site.

Or once you dock and fix the position of first ligand you can try docking t=
he second ligand.

HTH.

Regards,

Diwan



-----Original Message-----
> From: owner-chemistry:ccl.net [mailto:owner-chemistry:ccl.net]
Sent: Wednesday, August 06, 2008 1:33 AM
To: Abdul Hameed, MohamedDiwanMo
Subject: CCL: how I can dock two ligand at same site acive?





Sent to CCL by: =3D?utf-8?Q?_Jorge_Rodr=3DC3=3DADguez_Becerra?=3D [jorberr%=
x%ciq.uchile.cl]

Hi, I have a system that present two ligand in the same active site (pi-sta=
cking interactions between ligand). So, in the autodock 4 program I can`t u=
se this dimer system becouse autodock recognizes only one ligand of the dim=
er (a connectivity problem). If someone can help me. Because I don't knwon,=
 how I can dock two ligand at same site acive?



I will greatly appreciate it if someone helps me



Jorge R







-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--_000_62D3F106CB16C34D825A1B75EFBA683901697724CDEX7FM04adukye_
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<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Hi, <o:p></o:p></s=
pan></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>If you know how th=
e two
ligands bind, then you can divide the active site and do two separate docki=
ng.
i.e., (in case of autodock) you can define the grid such that it covers one
part of the active site and dock the ligand. Similarly you can dock the sec=
ond
ligand to the other half of active site. <o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Or once you dock a=
nd fix
the position of first ligand you can try docking the second ligand. &nbsp;<=
o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>HTH.<o:p></o:p></s=
pan></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Regards,<o:p></o:p=
></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Diwan<o:p></o:p></=
span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'><o:p>&nbsp;</o:p><=
/span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>-----Original
Message-----<br>
> From: owner-chemistry:ccl.net [mailto:owner-chemistry:ccl.net] <br>
Sent: Wednesday, August 06, 2008 1:33 AM<br>
To: Abdul Hameed, MohamedDiwanMo<br>
Subject: CCL: how I can dock two ligand at same site acive?<o:p></o:p></spa=
n></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'><o:p>&nbsp;</o:p><=
/span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'><o:p>&nbsp;</o:p><=
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<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Sent to CCL by:
=3D?utf-8?Q?_Jorge_Rodr=3DC3=3DADguez_Becerra?=3D [jorberr%x%ciq.uchile.cl]=
<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Hi, I have a syste=
m that
present two ligand in the same active site (pi-stacking interactions betwee=
n
ligand). So, in the autodock 4 program I can`t use this dimer system becous=
e
autodock recognizes only one ligand of the dimer (a connectivity problem). =
If
someone can help me. Because I don't knwon, how I can dock two ligand at sa=
me
site acive?<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'><o:p>&nbsp;</o:p><=
/span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>I will greatly
appreciate it if someone helps me<o:p></o:p></span></font></p>

<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'><o:p>&nbsp;</o:p><=
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<p class=3DMsoPlainText><font size=3D3 face=3D"Times New Roman"><span lang=
=3DEN-US
style=3D'font-size:12.0pt;font-family:"Times New Roman"'>Jorge R<o:p></o:p>=
</span></font></p>

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From owner-chemistry@ccl.net Thu Aug  7 16:32:02 2008
From: "Nicola Zonta nicola.zonta(-)gmail.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37511-080807092919-467-ydYI9r1F1OvkpDM+uEj6Qg:-:server.ccl.net>
X-Original-From: Nicola Zonta <nicola.zonta---gmail.com>
Content-Type: multipart/alternative; boundary=Apple-Mail-3--712992961
Date: Thu, 7 Aug 2008 14:32:55 +0200
Mime-Version: 1.0 (Apple Message framework v912)


Sent to CCL by: Nicola Zonta [nicola.zonta**gmail.com]

--Apple-Mail-3--712992961
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	charset=US-ASCII;
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Dear Arun,

have a look at Zodiac
www.zeden.org

it is still beta software, but you might find it useful. we've used it  
quite a lot for teaching purposes.
if you have any question please contact me

cheers
Nicola

On 7 Aug 2008, at 10:47, Arun Venkatnathan arunv1973|a|yahoo.com wrote:

> Dear All,
>
> I am looking for a free computational Chemistry software(s) which  
> works in Windows operating systems which can do simple ab initio  
> calculations as well as molecular mechanics. This will be used  
> primarily as a teaching tool for 2nd and 3rd year undergraduate  
> students.  Additionally, software which can display orbitals etc  
> will also be useful as a teaching tool.
>
> Any recommendations on choice of software for teaching or pointers  
> towards any free software will be deeply appreciated.
>
> Thanks,
> Arun
>
> Dr. Arun Venkatnathan
> Assistant Professor, Chemistry
> Indian Institute of Science Education and Research Pune
> India. 411021
> Tel: 91-20-2590-8044
>
>


--Apple-Mail-3--712992961
Content-Type: text/html;
	charset=US-ASCII
Content-Transfer-Encoding: quoted-printable

<html><body style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; =
-webkit-line-break: after-white-space; ">Dear Arun,<div><br =
class=3D"webkit-block-placeholder"></div><div>have a look at =
Zodiac</div><div><a =
href=3D"http://www.zeden.org">www.zeden.org</a></div><div><br =
class=3D"webkit-block-placeholder"></div><div>it is still beta software, =
but you might find it useful. we've used it quite a lot for teaching =
purposes.</div><div>if you have any question please contact =
me</div><div><br =
class=3D"webkit-block-placeholder"></div><div>cheers</div><div>Nicola&nbsp=
;</div><div><br><div><div>On 7 Aug 2008, at 10:47, Arun Venkatnathan =
arunv1973|a|yahoo.com wrote:</div><br =
class=3D"Apple-interchange-newline"><blockquote type=3D"cite"><table =
cellspacing=3D"0" cellpadding=3D"0" border=3D"0"><tbody><tr><td =
valign=3D"top" style=3D"font: inherit;">Dear All,<br><br>I am looking =
for a free computational Chemistry software(s) which works in Windows =
operating systems which can do simple ab initio calculations as well as =
molecular mechanics. This will be used primarily as a teaching tool for =
2nd and 3rd year undergraduate students.&nbsp; Additionally, software =
which can display orbitals etc will also be useful as a teaching tool. =
<br><br>Any recommendations on choice of software for teaching or =
pointers towards any free software will be deeply =
appreciated.<br><br>Thanks,<br>Arun <br><br>Dr. Arun =
Venkatnathan<br>Assistant Professor, Chemistry<br>Indian Institute of =
Science Education and Research Pune<br>India. 411021 <br>Tel: =
91-20-2590-8044<br><br></td></tr></tbody></table><br>       =
</blockquote></div><br></div></body></html>=

--Apple-Mail-3--712992961--


From owner-chemistry@ccl.net Thu Aug  7 17:11:01 2008
From: "John McKelvey jmmckel]![gmail.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37512-080807152918-24158-Rvk/GIof0+lKu4W83LdwyA^^server.ccl.net>
X-Original-From: "John McKelvey" <jmmckel(-)gmail.com>
Content-Type: multipart/alternative; 
	boundary="----=_Part_31036_13454685.1218133402508"
Date: Thu, 7 Aug 2008 14:23:22 -0400
MIME-Version: 1.0


Sent to CCL by: "John McKelvey" [jmmckel*o*gmail.com]
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ORCA is an extremely good free program  for academics containing both
semi-empirical [INDO/S, MNDO, AM1, PM3, and I think the only pure STO-based
NDDO method that follows Pople's original intent and also has analytical
derivatives,]  as well as _many_ DFT and TDDFT methodologies, and shares
many aspects with the very good commercial code TURBOMOLE (there is a lot of
code sharing between them).  It has very good support, and of course has
binaries available in many flavors of hardware/OS for (I think for MAC),
Windows, and Linux (AMD and Intel)  and I think some 32 and 64 bit versions.

Cheers,

John McKelvey

On Thu, Aug 7, 2008 at 10:09 AM, Alcides Simao alsimao(0)gmail.com <
owner-chemistry:-:ccl.net> wrote:

> Hello Arun!
>
> There are multiple software to choose from! But be CAREFUL with the
> licenses :)
>
> I personally recomend GAMESS!
>
> http://www.msg.ameslab.gov/GAMESS/
>
> GAMESS is fully featured on ab initio, semi-empiric and has the basis for
> MM calculations
>
> NWCHEM is another free, research-grade software, but it has a little more
> restrictive license.
>
> Another good package is ORCA
>
> http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php
>
> For DFT calculations, OCTOPUS ( http://www.tddft.org/ ) , as well as
> abinit (
> http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066) are
> good choices!
>
> Zodiac and Vega ZZ are good programs for Cheminformatics and MM work :)
> Tinker is also a good program!
>
> http://homepage.mac.com/swain/Macinchem/page11/page11.html <- Zodiac
> http://www.ddl.unimi.it/vega/index.htm <- Vega ZZ
> http://dasher.wustl.edu/tinker/ <- Tinker
>
> I hope this helps you :)
>

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<div dir="ltr">ORCA is an extremely good free program&nbsp; for academics
containing both semi-empirical [INDO/S, MNDO, AM1, PM3, and I think the only
pure STO-based NDDO method that follows Pople&#39;s original intent and
also has analytical derivatives,]&nbsp; as well as _many_ DFT and TDDFT
methodologies, and shares many aspects with the very good commercial
code TURBOMOLE (there is a lot of code sharing between them).&nbsp; It has
very good support, and of course has binaries available in many flavors
of hardware/OS for (I think for MAC), Windows, and Linux (AMD and
Intel)&nbsp; and I think some 32 and 64 bit versions.<br>
<br>Cheers,<br><font color="#888888"><br>John McKelvey</font><br><br><div class="gmail_quote">On Thu, Aug 7, 2008 at 10:09 AM, Alcides Simao alsimao(0)<a href="http://gmail.com">gmail.com</a> <span dir="ltr">&lt;<a href="mailto:owner-chemistry:-:ccl.net">owner-chemistry:-:ccl.net</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div dir="ltr">Hello Arun!<br><br>There are multiple software to choose from! But be CAREFUL with the licenses :)<br>
<br>I personally recomend GAMESS! <br><br><a href="http://www.msg.ameslab.gov/GAMESS/" target="_blank">http://www.msg.ameslab.gov/GAMESS/</a><br>
<br>GAMESS is fully featured on ab initio, semi-empiric and has the basis for MM calculations<br><br>NWCHEM is another free, research-grade software, but it has a little more restrictive license.<br><br>Another good package is ORCA<br>

<br><a href="http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php" target="_blank">http://ewww.mpi-muelheim.mpg.de/bac/logins/downloads_en.php</a><br><br>For DFT calculations, OCTOPUS ( <a href="http://www.tddft.org/" target="_blank">http://www.tddft.org/</a> ) , as well as abinit (<a href="http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066" target="_blank">http://www.atypon-link.com/OLD/doi/pdf/10.1524/zkri.220.5.558.65066</a>) are good choices!<br>

<br>Zodiac and Vega ZZ are good programs for Cheminformatics and MM work :) Tinker is also a good program!<br><br><a href="http://homepage.mac.com/swain/Macinchem/page11/page11.html" target="_blank">http://homepage.mac.com/swain/Macinchem/page11/page11.html</a> &lt;- Zodiac<br>

<a href="http://www.ddl.unimi.it/vega/index.htm" target="_blank">http://www.ddl.unimi.it/vega/index.htm</a> &lt;- Vega ZZ<br><a href="http://dasher.wustl.edu/tinker/" target="_blank">http://dasher.wustl.edu/tinker/</a> &lt;- Tinker<br>
<br>I hope this helps you :)<br>
</div>
</blockquote></div><br></div>

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From owner-chemistry@ccl.net Thu Aug  7 17:43:01 2008
From: "Ol Ga eurisco1|,|pochta.ru" <owner-chemistry=server.ccl.net>
To: CCL
Subject: CCL:G: Linux cluster for QM calculations
Message-Id: <-37513-080807170546-1258-KVP31wg1rEHoz9JSuRSxbg=server.ccl.net>
X-Original-From: "Ol  Ga" <eurisco1- -pochta.ru>
Date: Thu, 7 Aug 2008 17:05:42 -0400


Sent to CCL by: "Ol  Ga" [eurisco1(0)pochta.ru]
Dear Vivek Sharma,

I think that it is very important to define architecture (32- or 64-bit) of software/hardware which you will use for QC calculations. The 32-bit architecture has strong limitation in amount of memory. I think the best choice is 64-bit architecture of software/hardware. 
I intend that there are two variants (good and very good):
1) quad-core CPU + 8GB RAM (minimum) + GAUSSIAN 64-bit (only type %Nproc= and you will get parallelism)
2) dual-socket motherboard with 2 quad-core CPUs (=8 cores) + 16 GB RAM (minimum)+ GAUSSIAN 64-bit

You dont need 10 GB Ethernet adaptors in these cases  and you will get the small cluster in one box.

Sincerely,

Ol Ga

ps there are other QC program suites which have parallel executing.

----- Original Message ----- 
> From: "Vivek Sharma vivek.viv.sharma*gmail.com" <owner-chemistry^^^ccl.net>
To: "Ga, Ol " <eurisco1^^^pochta.ru>
Sent: Thursday, August 07, 2008 1:22 PM
Subject: CCL: Linux cluster for QM calculations

> Sent to CCL by: "Vivek  Sharma" [vivek.viv.sharma-,-gmail.com]
> Dear CCL people,
> 
> I have seen some emails on CCL; people asking about cluster/computer configurations for QM calculations, thus I also would like to know a bit. Actually, I would like to have a little feedback on the linux cluster we are building. We  because of lack of technical expertise, are keeping the things on low profile and would like to improve from there. The main idea is to have a separate cluster (which will be improved in due course of time) for QM calculations. We are starting with 2-node system:
> 
> a) 2.2 - 2.6GHz AMD Athlon per node.
> b) 3GB RAM per node.
> c) 160GB per node HDD.
> d) Server Class Motherboard per node and possibly extra-slots for increasing
> RAM and HDD capacity.
> e) Good graphics card per node.
> f) DVD ROM per node.
> g) 2 Ethernet adaptors per node.
> h) Misc: 1 Monitor, Cables, etc.
> 
> And, most probably we will be buying these machines of some BRAND (as we would like to have maintenance available in case of problems). And for OS also, we are thinking about RHEL 5 (with package for HPC) (again for maintenance reasons).
> 
> I apologise if details mentioned here are not-so-specific, but any input will be of great help. First question is that does this configuration sound decent, sure there is no-upper limit for QM calculations, but for starting purposes, does it look okay OR to say, where it seems utmost to improve, PROCESSORS or Memory (?). Secondly, how easy/difficult it is to further add-up the hardware, say nodes of different configuration from previous ones (?). Also, any little inputs regarding the possible programs, which can be parallelised easily over such a machine, will be helpful too.
> 
> Thanks very much in advance,
> 
> 
> Vivek Sharma
> vivek.viv.sharmaATgmail.com
> IMM, India.


From owner-chemistry@ccl.net Thu Aug  7 18:18:01 2008
From: "Oleg Trott trott|scripps.edu" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site acive?
Message-Id: <-37514-080807160050-17501-oL06UMTwNkbLmtknmmkdIA%a%server.ccl.net>
X-Original-From: "Oleg Trott" <trott{=}scripps.edu>
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Date: Thu, 7 Aug 2008 12:05:27 -0700
MIME-Version: 1.0


Sent to CCL by: "Oleg Trott" [trott##scripps.edu]
On Tue, Aug 5, 2008 at 10:32 PM, Jorge Rodr=EDguez Becerra
jorberr[*]ciq.uchile.cl <owner-chemistry===ccl.net> wrote:
>
> Sent to CCL by: =3D?utf-8?Q?_Jorge_Rodr=3DC3=3DADguez_Becerra?=3D [jorber=
r%x%ciq.uchile.cl]
> Hi, I have a system that present two ligand in the same active site (pi-s=
tacking interactions between ligand). So, in the autodock 4 program I can`t=
 use this dimer system becouse autodock recognizes only one ligand of the d=
imer (a connectivity problem). If someone can help me. Because I don't knwo=
n, how I can dock two ligand at same site acive?
>
> I will greatly appreciate it if someone helps me
>
> Jorge R


Shameless plug:

http://www.scripps.edu/~trott/vina/#tutorial

(Note that Vina is currently offered for evaluation only, and will
likely be non-free for commercial users)

--=20
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com


From owner-chemistry@ccl.net Thu Aug  7 18:56:01 2008
From: "Deskins, Nathaniel A nathaniel.deskins#%#pnl.gov" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Computational Chemistry software
Message-Id: <-37515-080807133042-28043-QB42uEgMSeBpRNGmPa3poQ- -server.ccl.net>
X-Original-From: "Deskins, Nathaniel A" <nathaniel.deskins|*|pnl.gov>
Content-class: urn:content-classes:message
Content-Type: multipart/alternative;
	boundary="----_=_NextPart_001_01C8F8AA.9EC60BE2"
Date: Thu, 7 Aug 2008 09:28:26 -0700
MIME-Version: 1.0


Sent to CCL by: "Deskins, Nathaniel A" [nathaniel.deskins..pnl.gov]

This is a multi-part message in MIME format.

------_=_NextPart_001_01C8F8AA.9EC60BE2
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	charset="US-ASCII"
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You might try NWchem. I believe there is a windows version, at least
through cygwin.
=20
Also, I think there is PC-Gamess.
=20
Arguslab lets you optimize at the semiempirical (AM1/PM3/MNDO) and MM
(UFF/Amber) levels. There are probably more semiempirical/MM codes
available for windows.=20
=20
Aaron

________________________________

> From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net]=20
Sent: Thursday, August 07, 2008 1:48 AM
To: Deskins, Nathaniel A
Subject: CCL: Computational Chemistry software


Dear All,

I am looking for a free computational Chemistry software(s) which works
in Windows operating systems which can do simple ab initio calculations
as well as molecular mechanics. This will be used primarily as a
teaching tool for 2nd and 3rd year undergraduate students.
Additionally, software which can display orbitals etc will also be
useful as a teaching tool.=20

Any recommendations on choice of software for teaching or pointers
towards any free software will be deeply appreciated.

Thanks,
Arun=20

Dr. Arun Venkatnathan
Assistant Professor, Chemistry
Indian Institute of Science Education and Research Pune
India. 411021=20
Tel: 91-20-2590-8044

=09


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	charset="US-ASCII"
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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=3Dus-ascii">
<META content=3D"MSHTML 6.00.6000.16674" name=3DGENERATOR></HEAD>
<BODY>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff>You might try NWchem. I believe there is a windows =
version, at=20
least through cygwin.</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff></FONT></SPAN>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff>Also, I think there is PC-Gamess.</FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff></FONT></SPAN>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff>Arguslab lets you optimize at the semiempirical =
(AM1/PM3/MNDO) and=20
MM (UFF/Amber) levels. There are probably more semiempirical/MM codes =
available=20
for windows. </FONT></SPAN></DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff></FONT></SPAN>&nbsp;</DIV>
<DIV dir=3Dltr align=3Dleft><SPAN class=3D460162216-07082008><FONT =
face=3DArial=20
color=3D#0000ff>Aaron</FONT></SPAN></DIV><BR>
<DIV class=3DOutlookMessageHeader lang=3Den-us dir=3Dltr align=3Dleft>
<HR tabIndex=3D-1>
<FONT face=3DTahoma size=3D2><B>From:</B> owner-chemistry%a%ccl.net=20
[mailto:owner-chemistry%a%ccl.net] <BR><B>Sent:</B> Thursday, August 07, =
2008 1:48=20
AM<BR><B>To:</B> Deskins, Nathaniel A<BR><B>Subject:</B> CCL: =
Computational=20
Chemistry software<BR></FONT><BR></DIV>
<DIV></DIV>
<TABLE cellSpacing=3D0 cellPadding=3D0 border=3D0>
  <TBODY>
  <TR>
    <TD vAlign=3Dtop>Dear All,<BR><BR>I am looking for a free =
computational=20
      Chemistry software(s) which works in Windows operating systems =
which can=20
      do simple ab initio calculations as well as molecular mechanics. =
This will=20
      be used primarily as a teaching tool for 2nd and 3rd year =
undergraduate=20
      students.&nbsp; Additionally, software which can display orbitals =
etc will=20
      also be useful as a teaching tool. <BR><BR>Any recommendations on =
choice=20
      of software for teaching or pointers towards any free software =
will be=20
      deeply appreciated.<BR><BR>Thanks,<BR>Arun <BR><BR>Dr. Arun=20
      Venkatnathan<BR>Assistant Professor, Chemistry<BR>Indian Institute =
of=20
      Science Education and Research Pune<BR>India. 411021 <BR>Tel:=20
      =
91-20-2590-8044<BR><BR></TD></TR></TBODY></TABLE><BR></BODY></HTML>

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From owner-chemistry@ccl.net Thu Aug  7 19:59:00 2008
From: "Oleg Trott trott~~scripps.edu" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site acive?
Message-Id: <-37516-080807195733-27021-SBxvc/JAXOs2+LjD45Y4zQ##server.ccl.net>
X-Original-From: "Oleg Trott" <trott(-)scripps.edu>
Content-Disposition: inline
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Date: Thu, 7 Aug 2008 16:57:21 -0700
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Sent to CCL by: "Oleg Trott" [trott]-[scripps.edu]
On Thu, Aug 7, 2008 at 9:31 AM, Abdul Hameed, MohamedDiwanMo
mabdu3!^!email.uky.edu

> ... once you dock and fix the position of first ligand you can try docking the second ligand.

This approach might not necessarily lead to an "optimal" arrangement
of the ligands. Think of the first ligand as a car that gets parked in
the middle of two adjacent parking spots, preventing the second driver
> from finding a spot.

Oleg

-- 
Oleg Trott, Ph.D. (Columbia University)

http://olegtrott.com


From owner-chemistry@ccl.net Thu Aug  7 20:35:01 2008
From: "Danni Harris danni===simbiosys.ca" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: how I can dock two ligand at same site active with autodock?
Message-Id: <-37517-080807182740-2682-3r3KwIhMrNa76QU7agVLTA**server.ccl.net>
X-Original-From: "Danni Harris" <danni!=!simbiosys.ca>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=iso-8859-1
Date: Thu, 7 Aug 2008 18:25:13 -0400 (EDT)
MIME-Version: 1.0


Sent to CCL by: "Danni Harris" [danni#simbiosys.ca]
Jorge

This is not a precise solution to your problem in that ideally one would
simultaneously dock both components of the pi-stacked dimers. With that
caveat as a preface, I happened to be interested in a problem underlying
non-classical inhibition in P450s ---with relevance non-sigmoidal kinetics
(and hetero- and homocooperativity  i.e. allosterism). I actually used an
approximate approach that involved a buildup procedure---that I termed
heirarchical docking the details of which are present in two papers:
Cheng D, Harris D, Reed JR, Backes WL.
Arch Biochem Biophys . 2007 Dec 15;468(2):174-82.
and

Arch Biochem Biophys . 2007 Jun 1;462(1):28-37

This involves an approximate buildup procedure---wherein you dock the 1st
component (ligand) then for 'each solution' prepare a set of grids for
that solution and dock the 2nd.

While I did this with autodock4---you could use this approach in principle
with any single ligand docking approach (Gold,eHiTS,Glide). I think a I
think that Jim Halpert's group and another group in Michigan has used such
an approach to get at phenomenology in non-competitive inhibition....

I would also add that eHiTS from SimBioSys has explicit scoring terms for
Pi-Pi stacking and Pi ----cation interactions---but I have never repeated
my recent P450 study with this approach (perhaps I should).

Again in closing I emphacize that iterative buildup procedure is not the
absolutely correct theoretical procedure---but as shown in the references
above it did shed light on the phenomenology underlying a set of
complementary competitive and non-competitive inhibition CYP2B4 studies in
Wayne Backes laboratory.

Best.

Dan Harris

"Jorge Rodriguez jorberr]_[ciq.uchile.cl" <owner-chemistry.**.ccl.net> wrote:


    Sent to CCL by: "Jorge Rodriguez" [jorberr++ciq.uchile.cl]
    Hi, I have a system that present two ligand in the same active site
(pi-stacking interactions between ligand). So, in the autodock 4
program I can`t use this dimer system becouse autodock recognizes only
one ligand of the dimer (a connectivity problem). If someone can help
me. Because I don't konw, how I can dock two ligand at same site
active?

    I will greatly appreciate it if someone helps me