From owner-chemistry@ccl.net Mon Jan 30 02:25:00 2006
From: "Kalju Kahn kalju(a)chem.ucsb.edu" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: suggestions for manual docking and building
Message-Id: <-30693-060130004602-29084-pHDsReG8D4F4ySgQbhdLdQ%%server.ccl.net>
X-Original-From: Kalju Kahn <kalju-*-chem.ucsb.edu>
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Date: Sun, 29 Jan 2006 21:45:53 -0800
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Sent to CCL by: Kalju Kahn [kalju__chem.ucsb.edu]
Dear Bruce, 

I have found SYBYL useful for such tasks.  It lacks some of your ideal
characteristics (not free, not Windows PC) but it is:

-direct.  You can mouse-maneuver easily the ligand or the protein or
both via intuitive global/local control toolbox.  

-easy loading.  Separate PDB files are loaded into different
overlapping molecular areas.  Once docked, the coordinates can be
merged and written out as a new PDB file.

-intuitive.  While SYBYL is not the easiest program to grasp, the
manual docking is very intuitive.  Ability to easily
display/hide/delete/color-code parts of the system help (e.g. hide all
but the residues within 6 A of active site is helpful).

-cheap platform that supports hardware stereo could be an used SGI
workstation or a newer Linux PC.  In practice, the docking can be done
reasonably well without 3D stereo.  

-the academic pricing for the SYBYL Base is reasonable if you find the
program useful for general modeling as well.

If cost is your main criterion, PyMOL might be a good candidate but I
had harder time figuring out how to perform manual docking with it.

Best wishes, 

Kalju  

-------------------
> Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
> Hi
> 
> I was wondering if people could suggest a good program for manually 

> and interactively building protein-ligand or nucleic acid-ligand  
> complexes.  Characteristics of the ideal program are:
> 
> - Direct.  I'd like to be able to grab one molecule and maneuver it 

> into a position I think is interesting using simple, direct mouse
and/ 
> or keyboard controls.
> 
> - Easily loaded.  The molecules - either macro or micro - would most
 
> likely come from different pdb files, though support of other
formats  
> would also be helpful.  A minimum of file preparation/conversion is 

> desirable.
> 
> - Intuitive.  The students who pass through my lab should be able to
 
> just pick it up and go; we need a tool to support our research,  
> rather than a system to dedicate our efforts to mastering.
> 
> - Available for common cheap platforms.  I'd like to use this on
PC's  
> in my lab or on my Mac laptop, or both.
> 
> - Supports hardware stereo.  It seems to me that that's the best way
 
> to build.
> 
> - Free.  Or cheap.  Or at least a good value worthy of an
investment.
> 
> I welcome all suggestions, and will summarize what I learn.
> 
> ciao,
> Bruce Palfey
> Department of Biological Chemistry
> University of Michigan Medical School
> Ann Arbor, MI 48109-0606> 
>
-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
-+
> 
> 
> 
> 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
University of California, Santa Barbara


From owner-chemistry@ccl.net Mon Jan 30 03:00:00 2006
From: "Don Steiger sd00_2002=-=yahoo.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: MD software question.
Message-Id: <-30694-060130015857-3083-ipYRUcFzzc1/5tu6+5bAXA ~ server.ccl.net>
X-Original-From: Don Steiger <sd00_2002_._yahoo.com>
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Date: Sun, 29 Jan 2006 21:58:52 -0800 (PST)
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Sent to CCL by: Don Steiger [sd00_2002/a\yahoo.com]
--- "Andrew FantFanttfantobopobox"
<owner-chemistry^ccl.ccl> wrote:

> Sent to CCL CCL Andrew FantFantntfantobopobox]
> MrceMrcel James both made good points that I won't
> bother duplicating here.  One 
> other thing to bear in mind is that while the
> math(s) involved in MD is 
> relatively straightforward, doing it efficiently
> usually isn't.  Even in 
> single-threaded code, there are a whole
> constellation of 
> tricks/shortcuts/advanced techniques that can make
> things go much faster (an 
> order of magnitude or more) compared to what a naive
> undergrad might achieve 
> left to their own devices.  


Could you elaborate on this.  There are integration
issues (sympsymplecticw, energy conservation), and
some form of cleverness for calculating long range
forces (e.g. fast multipole/tree methods, ...).  Ewald
sums show up alot are there more things that you can
add to this list?


>And when you get into
> parallel processing, it 
> becomes even more hairy.
> 
> Andy
> 
> -- 
> Andrew FantFant| And when the night is cloudy    |
> This space to let
> Molecular Geek | There is still a light         
> |----------------------
> fantfantobopobox | That shines on me               |
> Disclaimer:  I don't
> Boston, MA     | Shine until tomorrow, Let it be |
> even speak for myself
> 
> 
> 
> -= This is automatically added to each message by
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From owner-chemistry@ccl.net Mon Jan 30 03:35:00 2006
From: "David A. Case case-$-scripps.edu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: MD software question.
Message-Id: <-30695-060130021812-5156-eA8LMfjt548O/LFSy9iH9Q++server.ccl.net>
X-Original-From: "David A. Case" <case() scripps.edu>
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Sent to CCL by: "David A. Case" [case],[scripps.edu]
On Sun, Jan 29, 2006, JAMES VIVIAN jamestvivian()msn.com wrote:
> 
> You're basically correct that at the conceptual & mathematical level, things 
> are pretty straightforward;  you need to create & store ~3*N coordinates for 
> N particles, and F=ma tells the story.  So you then need an integrator.  And 
> a force-field.  And maybe a linked-list (Verlet), and some trickerly for 
> periodic-boundary conditions, etc.

The phrase "some trickery for periodic-boundary conditions" hides a lot
of pretty difficult code development.  The implementation of an accurate
(and efficient) technique such as PME and friends, (or the "fast multipole"
approach) for handling long-range electrostatics is quite complex.

I will also mention that many simulation codes are also coded to run in
parallel environments; this adds considerably to the code complexity.

Also, codes that include a QM/MM capability often effective have a quantum
chemistry program embedded into what is otherwise a classical MD environment.

...dave case


From owner-chemistry@ccl.net Mon Jan 30 05:00:01 2006
From: "Miklos Vargyas mvargyas[]chemaxon.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: suggestions for manual docking and building
Message-Id: <-30696-060130044442-12978-62q+mcOdTVhGie3Iq3WBzg{=}server.ccl.net>
X-Original-From: Miklos Vargyas <mvargyas^-^chemaxon.com>
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Date: Mon, 30 Jan 2006 09:47:50 +0100
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Sent to CCL by: Miklos Vargyas [mvargyas%chemaxon.com]
This is a multi-part message in MIME format.
--------------000401000009010909030008
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Dear Bruce.

you may wish to look at MarvinSpace by ChemAxon. 
<http://www.chemaxon.com/shared/MarvinSpace/>

1. Direct: select a small molecule loaded previously, then click the 
'Translate ligand'  button and use your mouse and keyboard to drag the 
molecule.

2. Easy load: MarvinSpace accepts pdb, mol, sdf, smiles, mol2, xyz, cml 
etc. Perceives bonds and bond types not defined in pdb, adds hydrogens 
and lone electron pairs.

3. Intuitive: I do hope so, though you can advice us how to improve it 
and we do the job.

4. It's java, runs on Win, Mac, Linux etc.

5. Stereo: not yet, but it's already in the pipe-line. Various stereo 
display modes will be available soon, including hardware, offaxis, 
cross-eye, parallel-eye.

6. Free. It is part of ChemAxon's Acedemic Package, follow link for 
details: http://www.chemaxon.com/forum/ftopic193.html

The easiest way to try MarvinSpace is via Java WebStart: go to the 
MarvinSpace demo page at http://www.chemaxon.com/shared/MarvinSpace/, 
there you'll find 4 screen snapshots that are buttons that launch 
MarvinSpace.
The software is also available as applet and standalone application.

I hope you find MarvinSpace interesting and suitable for your needs.

Regards,
Miklos Vargyas
ChemAxon Ltd.


Bruce Palfey brupalf|*|umich.edu wrote:

>Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
>Hi
>
>I was wondering if people could suggest a good program for manually  
>and interactively building protein-ligand or nucleic acid-ligand  
>complexes.  Characteristics of the ideal program are:
>
>- Direct.  I'd like to be able to grab one molecule and maneuver it  
>into a position I think is interesting using simple, direct mouse and/ 
>or keyboard controls.
>
>- Easily loaded.  The molecules - either macro or micro - would most  
>likely come from different pdb files, though support of other formats  
>would also be helpful.  A minimum of file preparation/conversion is  
>desirable.
>
>- Intuitive.  The students who pass through my lab should be able to  
>just pick it up and go; we need a tool to support our research,  
>rather than a system to dedicate our efforts to mastering.
>
>- Available for common cheap platforms.  I'd like to use this on PC's  
>in my lab or on my Mac laptop, or both.
>
>- Supports hardware stereo.  It seems to me that that's the best way  
>to build.
>
>- Free.  Or cheap.  Or at least a good value worthy of an investment.
>
>I welcome all suggestions, and will summarize what I learn.
>
>ciao,
>Bruce Palfey
>Department of Biological Chemistry
>University of Michigan Medical School
>Ann Arbor, MI 48109-0606>
>
>
>
>  
>

-- 
 
Miklos Vargyas, PhD
ChemAxon Ltd.
Maramaros koz 3/A, Budapest, 1037 Hungary

http://www.chemaxon.com
Cell: +3670 3813205
Tel: +361 4532661
Skype: miklos.vargyas
Fax: +361 4532659
e-mail: mvargyas+/-chemaxon.com <mailto:mvargyas+/-chemaxon.com>

--------------000401000009010909030008
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  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
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Dear Bruce.<br>
<br>
you may wish to look at MarvinSpace by ChemAxon. <a
 href="http://www.chemaxon.com/shared/MarvinSpace/"></a><br>
<br>
1. Direct: select a small molecule loaded previously, then click the
'Translate ligand'&nbsp; button and use your mouse and keyboard to drag the
molecule.<br>
<br>
2. Easy load: MarvinSpace accepts pdb, mol, sdf, smiles, mol2, xyz, cml
etc. Perceives bonds and bond types not defined in pdb, adds hydrogens
and lone electron pairs.<br>
<br>
3. Intuitive: I do hope so, though you can advice us how to improve it
and we do the job.<br>
<br>
4. It's java, runs on Win, Mac, Linux etc.<br>
<br>
5. Stereo: not yet, but it's already in the pipe-line. Various stereo
display modes will be available soon, including hardware, offaxis,
cross-eye, parallel-eye.<br>
<br>
6. Free. It is part of ChemAxon's Acedemic Package, follow link for
details: <a href="http://www.chemaxon.com/forum/ftopic193.html">http://www.chemaxon.com/forum/ftopic193.html</a><br>
<br>
The easiest way to try MarvinSpace is via Java WebStart: go to the
MarvinSpace demo page at <a
 href="http://www.chemaxon.com/shared/MarvinSpace/">http://www.chemaxon.com/shared/MarvinSpace/</a>,
there you'll find 4 screen snapshots that are buttons that launch
MarvinSpace. <br>
The software is also available as applet and standalone application.<br>
<br>
I hope you find MarvinSpace interesting and suitable for your needs.<br>
<br>
Regards,<br>
Miklos Vargyas<br>
ChemAxon Ltd.<br>
<br>
<br>
Bruce Palfey brupalf|*|umich.edu wrote:
<blockquote
 cite="mid-id%234ks-30687-060129154147-5198-+PuBWMeW6n3BXZDYsiUzyw+/-server.ccl.net"
 type="cite">
  <pre wrap="">Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
Hi

I was wondering if people could suggest a good program for manually  
and interactively building protein-ligand or nucleic acid-ligand  
complexes.  Characteristics of the ideal program are:

- Direct.  I'd like to be able to grab one molecule and maneuver it  
into a position I think is interesting using simple, direct mouse and/ 
or keyboard controls.

- Easily loaded.  The molecules - either macro or micro - would most  
likely come from different pdb files, though support of other formats  
would also be helpful.  A minimum of file preparation/conversion is  
desirable.

- Intuitive.  The students who pass through my lab should be able to  
just pick it up and go; we need a tool to support our research,  
rather than a system to dedicate our efforts to mastering.

- Available for common cheap platforms.  I'd like to use this on PC's  
in my lab or on my Mac laptop, or both.

- Supports hardware stereo.  It seems to me that that's the best way  
to build.

- Free.  Or cheap.  Or at least a good value worthy of an investment.

I welcome all suggestions, and will summarize what I learn.

ciao,
Bruce Palfey
Department of Biological Chemistry
University of Michigan Medical School
Ann Arbor, MI 48109-0606E-mail to subscribers: <a class="moz-txt-link-abbreviated" href="mailto:CHEMISTRY+/-ccl.net">CHEMISTRY+/-ccl.net</a> or use:
      <a class="moz-txt-link-freetext" href="http://www.ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>

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Before posting, check wait time at: <a class="moz-txt-link-freetext" href="http://www.ccl.net">http://www.ccl.net</a>

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Conferences: <a class="moz-txt-link-freetext" href="http://server.ccl.net/chemistry/announcements/conferences/">http://server.ccl.net/chemistry/announcements/conferences/</a>

Search Messages: <a class="moz-txt-link-freetext" href="http://www.ccl.net/htdig">http://www.ccl.net/htdig</a>  (login: ccl, Password: search)<a class="moz-txt-link-freetext" href="http://www.ccl.net/spammers.txt">http://www.ccl.net/spammers.txt</a>

RTFI: <a class="moz-txt-link-freetext" href="http://www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry/aboutccl/instructions/</a</pre>
</blockquote>
<br>
<div class="moz-signature">-- <br>
&nbsp;
<span style="color: rgb(153, 153, 153);"></span><br
 style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Miklos Vargyas, PhD
</span><br style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">ChemAxon Ltd.
</span><br style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Maramaros koz 3/A, Budapest,
1037 Hungary
</span><br style="color: rgb(153, 153, 153);">
<br style="color: rgb(153, 153, 153);">
<a href="http://www.chemaxon.com"><span
 style="color: rgb(153, 153, 153);"></span>http://www.chemaxon.com</a>
<br style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Cell: +3670 3813205
</span><br style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Tel: +361 4532661</span><br
 style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Skype: miklos.vargyas</span><br
 style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);">Fax: +361 4532659
</span><br style="color: rgb(153, 153, 153);">
<span style="color: rgb(153, 153, 153);"></span><span
 style="color: rgb(153, 153, 153);">e-mail: <a
 href="mailto:mvargyas+/-chemaxon.com">mvargyas+/-chemaxon.com</a></span>
</div>
</body>
</html>

--------------000401000009010909030008--


From owner-chemistry@ccl.net Mon Jan 30 06:31:01 2006
From: "Igor Avilov avilovi,averell.umh.ac.be" <owner-chemistry*|*server.ccl.net>
To: CCL
Subject: CCL:G: Problem with PCM in G03
Message-Id: <-30697-060130062800-9028-otuwQiYW0BkrR319p4MCgg*|*server.ccl.net>
X-Original-From: "Igor Avilov" <avilovi|-|averell.umh.ac.be>
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Date: Mon, 30 Jan 2006 11:40:13 +0100
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Sent to CCL by: "Igor Avilov" [avilovi() averell.umh.ac.be]
Dear CCL-ers,

I'm sorry for bothering you with yet another question about Gaussian.

I'd like to study the influence of the solvent on the UV/Vis spectra.

I use the following keywords:

# TD(Nstates=30) b3lyp/6-31g* SCRF(PCM,Read,Solvent=Acetonitrile) IOP(9/40=3) Test

During the calculations I get the following warnings:

.
.
 Warning! T(1538,1254)=0.75528838D+02 is big!
          T(1538,1538)=0.99493278D+02 T(1254,1254)=0.93314851D+01
 Warning! T(  77,2623)=0.75529729D+02 is big!
          T(  77,  77)=0.99494808D+02 T(2623,2623)=0.93318462D+01
 Error on total polarization charges =  0.02935
.
.

The calculations are successfully finished and the computed spectra are in good agreament with experiment.

However, I have some doubts, whether those warnings were poiting out to the fact that the results are unreliable or not. 

Last calculation using PCM model (on the geometry optimization in the triplet estate using unrestricted b3lyp) crashed with the following error message:

 Warning! T( 300, 251)=0.25920034D+02 is big!
          T( 300, 300)=0.19840160D+02 T( 251, 251)=0.28388188D+02
 Inv2 failed in DMIVCL.
 Error termination via Lnk1e in /cluster/apps/gaussian03_C02/x86_64-Linux/g03/l502.exe at Tue Jan 17 12:41:22 2006.
 Job cpu time:  0 days  2 hours 54 minutes  7.9 seconds.
 File lengths (MBytes):  RWF=    971 Int=      0 D2E=      0 Chk=     34 Scr=      1

Could anybody suggest how to avoid those warnings (if they indicate a serious problem) and the error during geometry optimization?

By the way, is there a page in the web, where the Gaussian warnings and errors are documented?

Best regards,
Igor Avilov.


From owner-chemistry@ccl.net Mon Jan 30 09:55:00 2006
From: "Luis Simon luissimonrubio,,hotmail.com" <owner-chemistry|a|server.ccl.net>
To: CCL
Subject: CCL:G: Program for geometry optimization using Hessian
Message-Id: <-30698-060130071923-31948-xapZ3yDRNfbhWXKW6Xwaog|a|server.ccl.net>
X-Original-From: "Luis  Simon" <luissimonrubio[A]hotmail.com>


Sent to CCL by: "Luis  Simon" [luissimonrubio+/-hotmail.com]
Dear all:

I have otained a transition state and I would like to study how the energy of this transition state is perturbed when some restrains (linking groups of this transition state) are added. From the hessian matrix (assuming harmonic potential energy surface) it is straightforward to obtain an energy function and calculate the increase in energy as a result of a small perturbation. I would like that this energy function could be added to an additional energy function (AMBER, MM2, etc) for the linking structure, so it could be possible to optimize the geometry of both fragments together. I have tried to define a force field based on diagonal elements of the hessian matrix (no cross terms, which I consider is a coarse aproximation and make the results dependent of the choice of internal coordinates) in gaussian, but I somehow failed. 

Is there any MM program that could accept an energy function obtained from a hessian matrix?

Thanks:

Luis Simn


From owner-chemistry@ccl.net Mon Jan 30 10:30:01 2006
From: "John McKelvey jmmckel~!~attglobal.net" <owner-chemistry+/-server.ccl.net>
To: CCL
Subject: CCL: MD software question.
Message-Id: <-30699-060130090027-7772-FA0b0RqRbeMADKOVT1Kp7w+/-server.ccl.net>
X-Original-From: John McKelvey <jmmckel,+,attglobal.net>
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Date: Mon, 30 Jan 2006 08:54:59 -0500
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Sent to CCL by: John McKelvey [jmmckel++attglobal.net]
Andrew,

You asked me some time ago about choice of basis sets for correlation 
calculations, and I have not answered.  I do not have a good answer.  I 
suppose there are the obvious things you already are aware of.. 
6-31G[d], 6311[d,p]... etc, the SVxP[d,p,f..] from T'mole, 
couple-cluster basis sets, augmented basis sets, etc..  I am just not up 
to speed on this.  You might lood into work of the T'mole people, among 
others.

BTW, if you want a very good, free QM package take a look at ORCA, by 
Frank Neese.

Best regards,

John McKelvey


Andrew Fant fant(~)pobox.com wrote:

>Sent to CCL by: Andrew Fant [fant]_[pobox.com]
>Mrcel and James both made good points that I won't bother duplicating here.  One 
>other thing to bear in mind is that while the math(s) involved in MD is 
>relatively straightforward, doing it efficiently usually isn't.  Even in 
>single-threaded code, there are a whole constellation of 
>tricks/shortcuts/advanced techniques that can make things go much faster (an 
>order of magnitude or more) compared to what a naive undergrad might achieve 
>left to their own devices.  And when you get into parallel processing, it 
>becomes even more hairy.
>
>Andy
>
>  
>


From owner-chemistry@ccl.net Mon Jan 30 11:05:00 2006
From: "CCL CCL computationalchemist*gmail.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: Most Widely Used UNIX commands
Message-Id: <-30700-060130062757-9009-d6BEdi8Y3+QPntd9Cq4tfw^_^server.ccl.net>
X-Original-From: CCL CCL <computationalchemist!^!gmail.com>
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Date: Mon, 30 Jan 2006 10:28:52 +0000
MIME-Version: 1.0


Sent to CCL by: CCL CCL [computationalchemist_-_gmail.com]
------=_Part_27711_33549942.1138616932107
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

Hi Folks,

I'm new to UNIX and to use cluster computing. I need help from you regardin=
g
the most widely used UNIX command for beowulf clusters. I have seen the
webpages and learnt the basic commands. But i'm not sure about the commands
that the computatinal chemist used ( to check the q system and so on)  I
will be helpful if i was poited to some useful web addresess, or given some
useful files.

Thanks in advance.

Regards,
sanjay

------=_Part_27711_33549942.1138616932107
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
Content-Disposition: inline

<div>Hi Folks,</div>
<div>&nbsp;</div>
<div>I'm new to UNIX and to use cluster computing. I need help from you reg=
arding the most widely used UNIX command for beowulf clusters. I have seen =
the webpages and learnt the basic commands. But i'm not sure about the comm=
ands that the computatinal chemist used ( to check the q system and so on) =
&nbsp;I will be helpful if i was poited to some useful web addresess, or gi=
ven some useful files.
</div>
<div>&nbsp;</div>
<div>Thanks in advance.</div>
<div>&nbsp;</div>
<div>Regards,</div>
<div>sanjay</div>

------=_Part_27711_33549942.1138616932107--


From owner-chemistry@ccl.net Mon Jan 30 11:39:01 2006
From: "Shobe, David dshobe[#]sud-chemieinc.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: OPT on large molecules
Message-Id: <-30701-060130101354-24008-sv9uuLmQtSBes8RvkxI0MA_._server.ccl.net>
X-Original-From: "Shobe, David" <dshobe[*]sud-chemieinc.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="iso-8859-1"
Date: Mon, 30 Jan 2006 16:13:37 +0100
MIME-Version: 1.0


Sent to CCL by: "Shobe, David" [dshobe.],[.sud-chemieinc.com]
We still haven't answered the main question: will the lack of optimization significantly effect the intramolecular charge transfer?  I'll assume here that the effect in question does not involve vibrational frequencies.

Even if the use of an arbitrary geometry doesn't materially change the results of the calculation, I would imagine you'd have some trouble convincing peer reviewers of that.  But there are some options (besides just being patient :-).

1. You could use molecualr mechanics to do the optimization
2. You could use an X-ray diffraction or other published structure, if one exists.
3. You could repeat the calculation at several geometries to demonstrate that, indeed, the calculated results do not have a significant dependence on molecular geometry.

The idea of checking whether the effect occurs at all, using an arbitrary but reasonable geometry, might not be a bad one.  After this investigational calculation, you could then decide whetehr it's worthwhile to redo the calculation with a proper geometry (and with all the other i's dotted and t's crossed, as it were).

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

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



-----Original Message-----
> From: owner-chemistry],[ccl.net [mailto:owner-chemistry],[ccl.net] 
Sent: Saturday, January 28, 2006 3:48 PM
To: Shobe, David
Subject: CCL: OPT on large molecules

Sent to CCL by: "David M. Close" [closed(_)etsu.edu]
  CCLers:
  I have a question about the necessity of optimizations.  I have uncovered an effect experimentally that involves changes in large molecules.  By large I mean that even partial optimizations with modest basis sets take several days.  The effect involves charge migration from one region of the molecule to another region.  I would like to examine this effect with computations.  After a weeks work I still don't have an answer because of the times taken to determine the optimized structures.
  I realize that the correct approach is to do calculations on the optimized structures.  For example, it is necessary to do frequency calculations on the optimized structures using the same basis sets in both calculations.  But what if one didn't use the optimized structures?  Suppose one only used a good guess at the optimized structure?  Would this cause the later calculations to be invalid?  Or might they be good enough to at least decide if the effect of interest is present and that actual optimizations are worthwhile?
  Regards, Dave Close.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. 
Thank you.


From owner-chemistry@ccl.net Mon Jan 30 12:15:00 2006
From: "Soisson, Stephen Michael stephen_soisson-x-merck.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: [ccp4bb]: Current Stereo 3D Display Info
Message-Id: <-30702-060130104829-14292-Sa6/pLt+sWuqjoTsFkOcxQ{=}server.ccl.net>
X-Original-From: "Soisson, Stephen Michael" <stephen_soisson*merck.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain
Date: Mon, 30 Jan 2006 10:02:37 -0500
MIME-Version: 1.0


Sent to CCL by: "Soisson, Stephen Michael" [stephen_soisson.[].merck.com]
I believe that even the large Phillips (22") that you list is no longer
being made and that what is in stock at places is just old inventory (could
be wrong though).  It is hard to believe, but these monitors just aren't
being made anymore.  We literally have people in our modeling group hording
these displays for a rainy day.  I've just given up on stereo and switched
to using higher-end LCD displays.  Less energy, less heat, and less eye
fatigue for me.

Steve

-----Original Message-----
> From: owner-ccp4bb[]dl.ac.uk [mailto:owner-ccp4bb[]dl.ac.uk] On Behalf Of
Warren DeLano
Sent: Saturday, January 28, 2006 2:59 PM
To: pymol-users[]lists.sourceforge.net
Cc: ccp4bb[]dl.ac.uk; vmd[]ks.uiuc.edu; pdb-l[]sdsc.edu;
o-info[]o-info.bioxray.dk; CCL Subscribers
Subject: [ccp4bb]: Current Stereo 3D Display Info


***  For details on how to be removed from this list visit the  ***
***          CCP4 home page http://www.ccp4.ac.uk         ***


Folks,

Whether you favor Macintosh, Linux, or Windows for stereo 3D
visualization, you're going to need some specific (and increasingly
rare) hardware.  

To help you find it, we've just updated our information page on
stereo-3D-capable displays, cards, emitters, and glasses:

http://pymol.sf.net/stereo3d.html

Remarkably, we can now only find one company selling a brand new CRT
monitor suitable for stereo 3D.  If you find any others, please do let
us know!

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:warren[]delsci.com      




------------------------------------------------------------------------------
Notice:  This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates (which may be known outside the United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as Banyu) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message.  If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.
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From owner-chemistry@ccl.net Mon Jan 30 12:50:04 2006
From: "Khan Amir Rafiq amirrafk\a/tcd.ie" <owner-chemistry]-[server.ccl.net>
To: CCL
Subject: CCL: [ccp4bb]: Current Stereo 3D Display Info
Message-Id: <-30703-060130112725-1807-/r9cjpIQUS9LJ2SyxJK2GQ]-[server.ccl.net>
X-Original-From: Khan Amir Rafiq <amirrafk _ tcd.ie>
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Date: Mon, 30 Jan 2006 15:26:09 +0000
MIME-Version: 1.0


Sent to CCL by: Khan Amir Rafiq [amirrafk- -tcd.ie]
I did not see the SGI C220 (flat screen CRT) listed, it works
nicely but is pricey..

Amir
Trinity College Dublin

Quoting "Soisson, Stephen Michael" <stephen_soisson]_[merck.com>:

> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> I believe that even the large Phillips (22") that you list is no longer
> being made and that what is in stock at places is just old inventory (could
> be wrong though).  It is hard to believe, but these monitors just aren't
> being made anymore.  We literally have people in our modeling group hording
> these displays for a rainy day.  I've just given up on stereo and switched
> to using higher-end LCD displays.  Less energy, less heat, and less eye
> fatigue for me.
>
> Steve
>
> -----Original Message-----
> From: owner-ccp4bb]_[dl.ac.uk [mailto:owner-ccp4bb]_[dl.ac.uk] On Behalf Of
> Warren DeLano
> Sent: Saturday, January 28, 2006 2:59 PM
> To: pymol-users]_[lists.sourceforge.net
> Cc: ccp4bb]_[dl.ac.uk; vmd]_[ks.uiuc.edu; pdb-l]_[sdsc.edu;
> o-info]_[o-info.bioxray.dk; CCL Subscribers
> Subject: [ccp4bb]: Current Stereo 3D Display Info
>
>
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
>
>
> Folks,
>
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.
>
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
>
> http://pymol.sf.net/stereo3d.html
>
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
>
> Cheers,
> Warren
>
> --
> Warren L. DeLano, Ph.D.
> Principal Scientist
>
> . DeLano Scientific LLC
> . 400 Oyster Point Blvd., Suite 213
> . South San Francisco, CA 94080 USA
> . Biz:(650)-872-0942  Tech:(650)-872-0834
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:warren]_[delsci.com
>
>
>
>
> ------------------------------------------------------------------------------
> Notice:  This e-mail message, together with any attachments, contains
> information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New
> Jersey, USA 08889), and/or its affiliates (which may be known outside the
> United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as
> Banyu) that may be confidential, proprietary copyrighted and/or legally
> privileged. It is intended solely for the use of the individual or entity
> named on this message.  If you are not the intended recipient, and have
> received this message in error, please notify us immediately by reply e-mail
> and then delete it from your system.
> ------------------------------------------------------------------------------
>
>


From owner-chemistry@ccl.net Mon Jan 30 13:24:00 2006
From: "John McKelvey jmmckel_-_attglobal.net" <owner-chemistry]*[server.ccl.net>
To: CCL
Subject: CCL: Previous Post Re Basis sets vs Correlation methods
Message-Id: <-30704-060130120529-19202-ohSOdf1nsQwvWmnz6MhPDg]*[server.ccl.net>
X-Original-From: John McKelvey <jmmckel%x%attglobal.net>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 30 Jan 2006 12:00:49 -0500
MIME-Version: 1.0


Sent to CCL by: John McKelvey [jmmckel^_^attglobal.net]
Folks,

First, apologies for the accidental CCL bandwidth for a personal message..

Also,  I am completely out of date relative to the methodology in this 
area, and clearly understand that there many good QM packages available 
that together cover a very large number of areas, and probably have 80% 
or larger commonality.  Some packages do things that others do not, as 
I'm sure you all know better than I.  They have a place.  So, my 
apologies if my comments have omitted reference the quality work that 
makes QM calculations so available and reliable in so many codes..

John McKelvey


From owner-chemistry@ccl.net Mon Jan 30 14:00:01 2006
From: "Rick Venable rvenable[A]pollux.cber.nih.gov" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Most Widely Used UNIX commands
Message-Id: <-30705-060130123900-15855-3Nj2zZwvCfCCfgRczsR8PQ(0)server.ccl.net>
X-Original-From: Rick Venable <rvenable#,#pollux.cber.nih.gov>
Content-Type: TEXT/PLAIN; charset=US-ASCII
Date: Mon, 30 Jan 2006 12:30:55 -0500
MIME-Version: 1.0


Sent to CCL by: Rick Venable [rvenable##pollux.cber.nih.gov]
On Mon, 30 Jan 2006, CCL CCL computationalchemist*gmail.com wrote:
> I'm new to UNIX and to use cluster computing. I need help from you
> regarding the most widely used UNIX command for beowulf clusters. I
> have seen the webpages and learnt the basic commands. But i'm not sure
> about the commands that the computatinal chemist used ( to check the q
> system and so on)  I will be helpful if i was poited to some useful
> web addresess, or given some useful files.

	Technically, those types of commands are not really Unix
commands per se, but tools designed to work in a Unix environment.
There are, in fact, a variety of such tools, and the choices made at
each site that sets up their own cluster can be fairly different.  You
should probably check with the sysadmin or other users of the specific
cluster for this information.

	For a number of Linux clusters, the PBS queueing system has seen
some popularity, with both open source and commercial versions available

open	http://www.OpenPbs.org/
comm	http://www.PBSPro.com/


-------------------------------------
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905  Rick_Venable AT nih*gov
ALT email:  rvenable AT speakeasy*org
-------------------------------------


From owner-chemistry@ccl.net Mon Jan 30 14:48:00 2006
From: "Elaine Meng meng|cgl.ucsf.edu" <owner-chemistry]![server.ccl.net>
To: CCL
Subject: CCL: suggestions for manual docking and building
Message-Id: <-30706-060130135757-28107-kG5VhhWi3X2YezC8xLlChw]![server.ccl.net>
X-Original-From: Elaine Meng <meng]*[cgl.ucsf.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=US-ASCII; format=flowed
Date: Mon, 30 Jan 2006 10:22:43 -0800
Mime-Version: 1.0 (Apple Message framework v746.2)


Sent to CCL by: Elaine Meng [meng:-:cgl.ucsf.edu]
Chimera might fill the bill, see
http://www.cgl.ucsf.edu/chimera/

- reads in PDB and Mol2 formats, among others

- each structure can be toggled between fixed and movable
with the mouse, using checkboxes below the command line
or in the Model Panel

- free for noncommercial use and available for Windows,
Mac (requires X11), Linux, etc.; easy download/install

- includes documentation and tutorials that can be
accessed from its Help menu


On Jan 29, 2006, at 1:49 PM, Bruce Palfey brupalf|*|umich.edu wrote:

> Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
> Hi
>
> I was wondering if people could suggest a good program for manually
> and interactively building protein-ligand or nucleic acid-ligand
> complexes.  Characteristics of the ideal program are:
>
> - Direct.  I'd like to be able to grab one molecule and maneuver it
> into a position I think is interesting using simple, direct mouse and/
> or keyboard controls.
>
> - Easily loaded.  The molecules - either macro or micro - would most
> likely come from different pdb files, though support of other formats
> would also be helpful.  A minimum of file preparation/conversion is
> desirable.
>
> - Intuitive.  The students who pass through my lab should be able to
> just pick it up and go; we need a tool to support our research,
> rather than a system to dedicate our efforts to mastering.
>
> - Available for common cheap platforms.  I'd like to use this on PC's
> in my lab or on my Mac laptop, or both.
>
> - Supports hardware stereo.  It seems to me that that's the best way
> to build.
>
> - Free.  Or cheap.  Or at least a good value worthy of an investment.
>
> I welcome all suggestions, and will summarize what I learn.
>
> ciao,
> Bruce Palfey
> Department of Biological Chemistry
> University of Michigan Medical School
> Ann Arbor, MI 48109-0606
>

-----
Elaine C. Meng, Ph.D.                          meng,cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


From owner-chemistry@ccl.net Mon Jan 30 15:23:01 2006
From: "Harald Lanig Harald.Lanig/a\chemie.uni-erlangen.de" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL: Distance restraints in NAMD
Message-Id: <-30707-060130143434-21976-ii+tHa2knB4WMSV54aO/WA||server.ccl.net>
X-Original-From: Harald Lanig <Harald.Lanig[a]chemie.uni-erlangen.de>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 30 Jan 2006 19:33:54 +0100
MIME-Version: 1.0


Sent to CCL by: Harald Lanig [Harald.Lanig-#-chemie.uni-erlangen.de]
Dear CCL list members,

I want to restraint several atom-atom distances during a MD simulation 
with NAMD. Searching the manual and the web site, I found no solution to 
this (in my eyes not very unusual) problem. Constraining/fixing atoms to 
positions in cartesian space is implemented and works fine...

Can anyone out there please help me to solve this problem?! Any help is 
highly appreciated!

Thanks a lot!
-Harry

-- 
------------------------------------------------------------------------
  Dr. Harald Lanig            Universitaet Erlangen/Nuernberg
  Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

  Phone +49(0)9131-85 26525   email: lanig AT chemie.uni-erlangen.de
  Fax   +49(0)9131-85 26565   http://www.ccc.uni-erlangen.de/lanig
------------------------------------------------------------------------


From owner-chemistry@ccl.net Mon Jan 30 16:04:01 2006
From: "TJ O Donnell tjo .. gnova.com" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: [ccp4bb]: Current Stereo 3D Display Info
Message-Id: <-30708-060130150201-7424-MnBHrtrGKrx3ioJ2o5B+3Q{}server.ccl.net>
X-Original-From: "TJ O'Donnell" <tjo:_:gnova.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Mon, 30 Jan 2006 10:52:59 -0800
MIME-Version: 1.0


Sent to CCL by: "TJ O'Donnell" [tjo/a\gnova.com]
Does anyone have experience with LCD stereo displays, such as the
ones here?
http://www.stereo3d.com/displays.htm

I know this has been discussed before, but you don't have to give up
on stereo to use an LCD display.  It is possible to train your eyes
to see cross-eyed or wall-eyed stereo using two side-by-side images.
One can also use a simple, but specially-made viewing box with mirrors.
I may have plans for this around somewhere in 20 year old folders!
We used to do this before image alternating stereo displays were feasible.
Strange, that things seem to be regressing.

TJ
-- 
TJ O'Donnell, Ph.D.
gNova Scientific Software
http://www.gnova.com/
619 251 8304
619 255 2522 (fax)

Soisson, Stephen Michael stephen_soisson-x-merck.com wrote:
> Sent to CCL by: "Soisson, Stephen Michael" [stephen_soisson.() .merck.com]
> I believe that even the large Phillips (22") that you list is no longer
> being made and that what is in stock at places is just old inventory (could
> be wrong though).  It is hard to believe, but these monitors just aren't
> being made anymore.  We literally have people in our modeling group hording
> these displays for a rainy day.  I've just given up on stereo and switched
> to using higher-end LCD displays.  Less energy, less heat, and less eye
> fatigue for me.
> 
> Steve
> 
> -----Original Message-----
> 
>>From: owner-ccp4bb],[dl.ac.uk [mailto:owner-ccp4bb],[dl.ac.uk] On Behalf Of
> 
> Warren DeLano
> Sent: Saturday, January 28, 2006 2:59 PM
> To: pymol-users],[lists.sourceforge.net
> Cc: ccp4bb],[dl.ac.uk; vmd],[ks.uiuc.edu; pdb-l],[sdsc.edu;
> o-info],[o-info.bioxray.dk; CCL Subscribers
> Subject: [ccp4bb]: Current Stereo 3D Display Info
> 
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> 
> Folks,
> 
> Whether you favor Macintosh, Linux, or Windows for stereo 3D
> visualization, you're going to need some specific (and increasingly
> rare) hardware.  
> 
> To help you find it, we've just updated our information page on
> stereo-3D-capable displays, cards, emitters, and glasses:
> 
> http://pymol.sf.net/stereo3d.html
> 
> Remarkably, we can now only find one company selling a brand new CRT
> monitor suitable for stereo 3D.  If you find any others, please do let
> us know!
> 
> Cheers,
> Warren
> 
> --
> Warren L. DeLano, Ph.D.                     
> Principal Scientist
> 
> . DeLano Scientific LLC  
> . 400 Oyster Point Blvd., Suite 213           
> . South San Francisco, CA 94080 USA   
> . Biz:(650)-872-0942  Tech:(650)-872-0834     
> . Fax:(650)-872-0273  Cell:(650)-346-1154
> . mailto:warren],[delsci.com      
> 
> 
>


From owner-chemistry@ccl.net Mon Jan 30 18:17:00 2006
From: "Dr. Peter Bladon cbas25:+:strath.ac.uk" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL: Stereo display
Message-Id: <-30709-060130175507-2965-8tlCOveDtdhP1Qvbt71e9g#server.ccl.net>
X-Original-From: "Dr. Peter Bladon" <cbas25]![strath.ac.uk>
Content-Type: multipart/alternative;
 boundary="------------040901060003010304080709"
Date: Mon, 30 Jan 2006 22:48:45 +0000
MIME-Version: 1.0


Sent to CCL by: "Dr. Peter Bladon" [cbas25]_[strath.ac.uk]
This is a multi-part message in MIME format.
--------------040901060003010304080709
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit

Dear Modellers,  (Sorry 2 l's)

There is a solution to the problems of the demise of CRT displays.

This involves the use of a pair of LCD projectors.  I have been thinking 
about this for some time, but only this week the mail-order distributor 
CPC in Preston, England has advertised a DLP projector for 499.50 GB 
pounds (roughly $750 US). What makes these interesting is the claim that 
they support SXGA (1280x1024) resolution. Two of these fitted with 
polarisers on the front of the lenses, connected to two display ports on 
a suitably programmed computer, focussed and superimposed on a (silver 
not beaded) screen, and viewed through inexpensive polarising spectacles 
would give the equivalent of what has traditionally been used to view 
stereo (photo) slides.

The only bit missing is the necessary software to drive the display 
cards; maybe that has been solved already?

The advantage of this approach is that it allows for viewing by groups 
of people without the expense of shutter spectacles. 

Peter Bladon
Interprobe Chemical Services
Gallowhill House,  Larch Avenue
Lenzie,   Kirkintilloch
Glasgow  G66 4HX
Scotland

Phone:   +44-(0)141-578-1109
Fax:     +44-(0)141-776-7712
URL:     http://www.interprobe.co.uk/inter/interprobe.html

--------------040901060003010304080709
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
<font size="+1"><tt>Dear Modellers,&nbsp; (Sorry 2 l's)<br>
<br>
There is a solution to the problems of the demise of CRT displays. <br>
<br>
This involves the use of a pair of LCD projectors.&nbsp; I have been
thinking about this for some time, but only this week the mail-order
distributor CPC in Preston, England has advertised a DLP projector for
499.50 GB pounds (roughly $750 US). What makes these interesting is the
claim that they support SXGA (1280x1024) resolution. Two of these
fitted with polarisers on the front of the lenses, connected to two
display ports on a suitably programmed computer, focussed and
superimposed on a (silver not beaded) screen, and viewed through
inexpensive polarising spectacles would give the equivalent of what has
traditionally been used to view stereo (photo) slides.<br>
<br>
The only bit missing is the necessary software to drive the display
cards; maybe that has been solved already?<br>
<br>
The advantage of this approach is that it allows for viewing by groups
of people without the expense of shutter spectacles.&nbsp; <br>
<br>
Peter Bladon<br>
Interprobe Chemical Services<br>
Gallowhill House,&nbsp; Larch Avenue<br>
Lenzie,&nbsp;&nbsp; Kirkintilloch<br>
Glasgow&nbsp; G66 4HX<br>
Scotland<br>
<br>
Phone:&nbsp;&nbsp; +44-(0)141-578-1109<br>
Fax:&nbsp;&nbsp;&nbsp;&nbsp; +44-(0)141-776-7712<br>
URL:&nbsp;&nbsp; &nbsp; <a class="moz-txt-link-freetext" href="http://www.interprobe.co.uk/inter/interprobe.html">http://www.interprobe.co.uk/inter/interprobe.html</a> <br>
</tt></font>
</body>
</html>

--------------040901060003010304080709--


From owner-chemistry@ccl.net Mon Jan 30 18:52:01 2006
From: "mol2mol mol2mol2006(_)interware.hu" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL:G: Mol2mol 5.5 available
Message-Id: <-30710-060130161917-11284-tZcOuntb3vVg6RwthIMQog|,|server.ccl.net>
X-Original-From: "mol2mol" <mol2mol2006|interware.hu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	format=flowed;
	charset="iso-8859-2";
	reply-type=original
Date: Mon, 30 Jan 2006 21:22:16 +0100
MIME-Version: 1.0


Sent to CCL by: "mol2mol" [mol2mol2006(a)interware.hu]
Dear CCL Members,

    The new 5.5.0 version of the molecule file conversion,
manipulation and utility program Mol2Mol is now available
> from http://web.interware.hu/frenzy/mol2mol as trial or
shareware version.
    The current version of Mol2Mol recognizes, and interconverts
about 50 different file formats (including subtypes). By entering
a format string practically every Cartesian or MOPAC type Z matrix
formats can be out/inputted (even in polar coordinates).

 It can slice multiple structural files to single ones (such 
as PDB models or MDL SD files to single ones) and vice versa
in several variations. Support for PDB Chime subformat
(with 1-2-3 bonds). Many molecular utilities.

**New in Mol2mol 5.5:**

- New file types:
    Molden format (read)
    Turbomole input format (read) and *.cosmo output (read)
        (feedbacks are wellcomed)

- Gamess and Q-Chem input files are now recognized as normal
files, and they can be copied and inputted via the clipboard, too.

- User defined input/output formats: now 16-16 format strings can
be defined and saved, respectively, and recall or edit later. This
can be very handy when coordinates should be cut and paste
> from e.g. e-mails or unsupported files to Mol2mol.

- Background color can be set to any color now.

- Several small corrections, bug fixes were also made.


**In the previous version Mol2Mol 5.4:**

- Input of Gaussian output files (now recognized automatically);
- Input of Gamess output files (now recognized automatically);
    (the structures one by one or in browse mode (with charges added))

-  Support has been added for the Jmol java applet: MDL mol, XMOL xyz
and HyperChem hin files can be written as a javascript
variable for using them as inline molecules in html files.

   Mol2mol is a very handy set of tools for everybody dealing with
molecular modelling.
   It is impossible to write here all of the features of Mol2Mol,
but have a look at its home page:

http://web.interware.hu/frenzy/mol2mol
e-mail: mol2mol2006 {at} interware.hu

POV-Ray fans may also have a look at:
http://dragon.unideb.hu/~gundat/povraya.htm 

The program is available as 30 days unrestricted trial version or
as shareware version.


From owner-chemistry@ccl.net Mon Jan 30 19:27:00 2006
From: "Abrash, Samuel sabrash/a\richmond.edu" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL: [Bad Mail]RE: OPT on large molecules
Message-Id: <-30711-060130150201-742123-0Z7+jbSqWtt9gqWMQqMaaA|,|server.ccl.net>
X-Original-From: "Abrash, Samuel" <sabrash a richmond.edu>
Date: Mon, 30 Jan 2006 13:04:03 -0500


Sent to CCL by: "Abrash, Samuel" [sabrash!=!richmond.edu]

Could you use quantum monte carlo to do the optimization?
 
Sam

        -----Original Message----- 
        From: Shobe, David dshobe[#]sud-chemieinc.com [mailto:owner-chemistry.:.ccl.net] 
        Sent: Mon 1/30/2006 12:14 PM 
        To: Abrash, Samuel 
        Cc: 
        Subject: CCL: OPT on large molecules
        
        

        Sent to CCL by: "Shobe, David" [dshobe..:..sud-chemieinc.com]
        We still haven't answered the main question: will the lack of optimization
significantly effect the intramolecular charge transfer?  I'll assume here that the
effect in question does not involve vibrational frequencies.
        
        Even if the use of an arbitrary geometry doesn't materially change the results of
the calculation, I would imagine you'd have some trouble convincing peer reviewers
of that.  But there are some options (besides just being patient :-).
        
        1. You could use molecualr mechanics to do the optimization
        2. You could use an X-ray diffraction or other published structure, if one exists.
        3. You could repeat the calculation at several geometries to demonstrate that,
indeed, the calculated results do not have a significant dependence on molecular
geometry.
        
        The idea of checking whether the effect occurs at all, using an arbitrary but
reasonable geometry, might not be a bad one.  After this investigational
calculation, you could then decide whetehr it's worthwhile to redo the calculation
with a proper geometry (and with all the other i's dotted and t's crossed, as it
were).
        
        --David Shobe, Ph.D., M.L.S.
        Süd-Chemie, Inc.
        phone (502) 634-7409
        fax (502) 634-7724
        
        Don't bother flaming me: I'm behind a firewall.
        
        
        
        -----Original Message-----
        > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net]

        Sent: Saturday, January 28, 2006 3:48 PM
        To: Shobe, David
        Subject: CCL: OPT on large molecules
        
        Sent to CCL by: "David M. Close" [closed(_)etsu.edu]
          CCLers:
          I have a question about the necessity of optimizations.  I have uncovered an
effect experimentally that involves changes in large molecules.  By large I mean
that even partial optimizations with modest basis sets take several days.  The
effect involves charge migration from one region of the molecule to another
region.  I would like to examine this effect with computations.  After a weeks
work I still don't have an answer because of the times taken to determine the
optimized structures.
          I realize that the correct approach is to do calculations on the optimized
structures.  For example, it is necessary to do frequency calculations on the
optimized structures using the same basis sets in both calculations.  But what if
one didn't use the optimized structures?  Suppose one only used a good guess at
the optimized structure?  Would this cause the later calculations to be invalid? 
Or might they be good enough to at least decide if the effect of interest is
present and that actual optimizations are worthwhile?
          Regards, Dave Close.

[Edited by jkl.:.ccl.net to removed winmail.dat attachment]


From owner-chemistry@ccl.net Mon Jan 30 20:02:01 2006
From: "Warren DeLano warren:delsci.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Stereo display
Message-Id: <-30712-060130185146-24024-DvEGgJYaFwvd93ROUU44Vw]|[server.ccl.net>
X-Original-From: "Warren DeLano" <warren=-=delsci.com>
Content-class: urn:content-classes:message
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Mon, 30 Jan 2006 15:53:50 -0800
MIME-Version: 1.0


Sent to CCL by: "Warren DeLano" [warren(0)delsci.com]
Peter, 

> The only bit missing is the necessary software to drive the 
> display cards; maybe that has been solved already?

On Linux at least, dual-headed nVidia Quadro cards support a special
stereo clone mode for precisely this situation.  It is 100% compatible
with existing stereo 3D software using the OpenGL quadbuffer API, and so
one digital projector simply gets the left image while the other gets
the right.  Both projectors display the non-stereo content, so the
effect is exactly like using shutter glasses on a CRT with
stereo-3D-in-a-window.

I don't know if that same capability is available yet on Windows or Mac,
but it is a great solution for building inexpensive "geowalls" with full
stereo 3D software compatiblity.

Cheers,
Warren

--
Warren L. DeLano, Ph.D.                     
Principal Scientist

. DeLano Scientific LLC  
. 400 Oyster Point Blvd., Suite 213           
. South San Francisco, CA 94080 USA   
. Biz:(650)-872-0942  Tech:(650)-872-0834     
. Fax:(650)-872-0273  Cell:(650)-346-1154
. mailto:warren]_[delsci.com      
 

> -----Original Message-----
> From: owner-chemistry]_[ccl.net [mailto:owner-chemistry]_[ccl.net] 
> Sent: Monday, January 30, 2006 3:41 PM
> To: Warren DeLano
> Subject: CCL: Stereo display
> 
> Sent to CCL by: "Dr. Peter Bladon" [cbas25]_[strath.ac.uk] 
> This is a multi-part message in MIME format.
> --------------040901060003010304080709
> Content-Type: text/plain; charset=us-ascii; format=flowed
> Content-Transfer-Encoding: 7bit
> 
> Dear Modellers,  (Sorry 2 l's)
> 
> There is a solution to the problems of the demise of CRT displays.
> 
> This involves the use of a pair of LCD projectors.  I have 
> been thinking about this for some time, but only this week 
> the mail-order distributor CPC in Preston, England has 
> advertised a DLP projector for 499.50 GB pounds (roughly $750 
> US). What makes these interesting is the claim that they 
> support SXGA (1280x1024) resolution. Two of these fitted with 
> polarisers on the front of the lenses, connected to two 
> display ports on a suitably programmed computer, focussed and 
> superimposed on a (silver not beaded) screen, and viewed 
> through inexpensive polarising spectacles would give the 
> equivalent of what has traditionally been used to view stereo 
> (photo) slides.
> 
> The only bit missing is the necessary software to drive the 
> display cards; maybe that has been solved already?
> 
> The advantage of this approach is that it allows for viewing 
> by groups of people without the expense of shutter spectacles. 
> 
> Peter Bladon
> Interprobe Chemical Services
> Gallowhill House,  Larch Avenue
> Lenzie,   Kirkintilloch
> Glasgow  G66 4HX
> Scotland
> 
> Phone:   +44-(0)141-578-1109
> Fax:     +44-(0)141-776-7712
> URL:     http://www.interprobe.co.uk/inter/interprobe.html
> 
> --------------040901060003010304080709
> Content-Type: text/html; charset=us-ascii
> Content-Transfer-Encoding: 7bit
> 
> <!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 
> Transitional//EN"> <html> <head>
>   <meta content="text/html;charset=ISO-8859-1" 
> http-equiv="Content-Type">
>   <title></title>
> </head>
> <body bgcolor="#ffffff" text="#000000">
> <font size="+1"><tt>Dear Modellers,&nbsp; (Sorry 2 l's)<br> 
> <br> There is a solution to the problems of the demise of CRT 
> displays. <br> <br> This involves the use of a pair of LCD 
> projectors.&nbsp; I have been thinking about this for some 
> time, but only this week the mail-order distributor CPC in 
> Preston, England has advertised a DLP projector for 499.50 GB 
> pounds (roughly $750 US). What makes these interesting is the 
> claim that they support SXGA (1280x1024) resolution. Two of 
> these fitted with polarisers on the front of the lenses, 
> connected to two display ports on a suitably programmed 
> computer, focussed and superimposed on a (silver not beaded) 
> screen, and viewed through inexpensive polarising spectacles 
> would give the equivalent of what has traditionally been used 
> to view stereo (photo) slides.<br> <br> The only bit missing 
> is the necessary software to drive the display cards; maybe 
> that has been solved already?<br> <br> The advantage of this 
> approach is that it allows for viewing by groups of people 
> without the expense of shutter spectacles.&nbsp; <br> <br> 
> Peter Bladon<br> Interprobe Chemical Services<br> Gallowhill 
> House,&nbsp; Larch Avenue<br> Lenzie,&nbsp;&nbsp; 
> Kirkintilloch<br> Glasgow&nbsp; G66 4HX<br> Scotland<br> <br> 
> Phone:&nbsp;&nbsp; +44-(0)141-578-1109<br> 
> Fax:&nbsp;&nbsp;&nbsp;&nbsp; +44-(0)141-776-7712<br> 
> URL:&nbsp;&nbsp; &nbsp; <a class="moz-txt-link-freetext" 
> href="http://www.interprobe.co.uk/inter/interprobe.html">http:
//www.interprobe.co.uk/inter/interprobe.html</a> <br> </tt></font>
</body> </html>
> 
> --------------040901060003010304080709--
> 
> 
> 
> -= 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 Mon Jan 30 20:37:01 2006
From: "Dr. Peter Bladon cbas25-$-strath.ac.uk" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: suggestions for manual docking and building
Message-Id: <-30713-060130195639-26786-pzT5OgVGz/sw5S9TD+XpSQ++server.ccl.net>
X-Original-From: "Dr. Peter Bladon" <cbas25:-:strath.ac.uk>
Content-Type: multipart/alternative;
 boundary="------------090904010900080300060500"
Date: Tue, 31 Jan 2006 00:50:17 +0000
MIME-Version: 1.0


Sent to CCL by: "Dr. Peter Bladon" [cbas25[A]strath.ac.uk]
This is a multi-part message in MIME format.
--------------090904010900080300060500
Content-Type: text/plain; charset=us-ascii; format=flowed
Content-Transfer-Encoding: 7bit



Bruce Palfey brupalf|*|umich.edu wrote:

>Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
>Hi
>
>I was wondering if people could suggest a good program for manually  
>and interactively building protein-ligand or nucleic acid-ligand  
>complexes.  Characteristics of the ideal program are:
>
>- Direct.  I'd like to be able to grab one molecule and maneuver it  
>into a position I think is interesting using simple, direct mouse and/ 
>or keyboard controls.
>
>- Easily loaded.  The molecules - either macro or micro - would most  
>likely come from different pdb files, though support of other formats  
>would also be helpful.  A minimum of file preparation/conversion is  
>desirable.
>
>- Intuitive.  The students who pass through my lab should be able to  
>just pick it up and go; we need a tool to support our research,  
>rather than a system to dedicate our efforts to mastering.
>
>- Available for common cheap platforms.  I'd like to use this on PC's  
>in my lab or on my Mac laptop, or both.
>
>- Supports hardware stereo.  It seems to me that that's the best way  
>to build.
>
>- Free.  Or cheap.  Or at least a good value worthy of an investment.
>
>I welcome all suggestions, and will summarize what I learn.
>
>ciao,
>Bruce Palfey
>Department of Biological Chemistry
>University of Michigan Medical School
>Ann Arbor, MI 48109-0606
>
>  
>
Interchem-Pc has facilities for manual docking. It is free to 
academics.  You would need the auxiliary program for converting PDB 
files to Interchem format.

All of the Interprobe software is described on:

http://www.interprobe.co.uk/inter/interprobe.html  

This website has a link to the site from where you can download the 
software.

Peter Bladon

Interprobe Chemical Services
Gallowhill House,  Larch Avenue
Lenzie, Kirkintilloch
Glasgow G66 4HX
Scotland




> 
>


--------------090904010900080300060500
Content-Type: text/html; charset=us-ascii
Content-Transfer-Encoding: 7bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
<br>
<br>
Bruce Palfey brupalf|*|umich.edu wrote:
<blockquote
 cite="mid-id%233qq-30687-060129154147-5198-HpAarxX1s+5x3Snd3ApjBg---server.ccl.net"
 type="cite">
  <pre wrap="">Sent to CCL by: Bruce Palfey [brupalf^-^umich.edu]
Hi

I was wondering if people could suggest a good program for manually  
and interactively building protein-ligand or nucleic acid-ligand  
complexes.  Characteristics of the ideal program are:

- Direct.  I'd like to be able to grab one molecule and maneuver it  
into a position I think is interesting using simple, direct mouse and/ 
or keyboard controls.

- Easily loaded.  The molecules - either macro or micro - would most  
likely come from different pdb files, though support of other formats  
would also be helpful.  A minimum of file preparation/conversion is  
desirable.

- Intuitive.  The students who pass through my lab should be able to  
<font face="Courier New, Courier, monospace">just pick it up and go; we need a tool to support our research,  
rather than a system to dedicate our efforts to mastering.

- Available for common cheap platforms.  I'd like to use this on PC's  
in my lab or on my Mac laptop, or both.

- Supports hardware stereo.  It seems to me that that's the best way  
to build.

- Free.  Or cheap.  Or at least a good value worthy of an investment.

I welcome all suggestions, and will summarize what I learn.

ciao,
Bruce Palfey
Department of Biological Chemistry
University of Michigan Medical School
Ann Arbor, MI 48109-0606
</font>
  </pre>
</blockquote>
<font face="Courier New, Courier, monospace"><small>Interchem-Pc has
facilities for manual docking. It is free to academics.&nbsp; You would need
the auxiliary program for converting PDB files to Interchem format.<br>
<br>
All of the Interprobe software is described on:<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.interprobe.co.uk/inter/interprobe.html">http://www.interprobe.co.uk/inter/interprobe.html</a>&nbsp;&nbsp; <br>
<br>
This website has a link to the site from where you can download the
software.<br>
<br>
Peter Bladon<br>
<br>
Interprobe Chemical Services<br>
Gallowhill House,&nbsp; Larch Avenue<br>
Lenzie, Kirkintilloch<br>
Glasgow G66 4HX<br>
Scotland<br>
<br>
</small><br>
<br>
<br>
</font>
<blockquote
 cite="mid-id%233qq-30687-060129154147-5198-HpAarxX1s+5x3Snd3ApjBg---server.ccl.net"
 type="cite">
  <pre wrap=""> </pre>
</blockquote>
<br>
</body>
</html>

--------------090904010900080300060500--


From owner-chemistry@ccl.net Mon Jan 30 21:26:01 2006
From: "Alexander Kollias ackollias[*]gmail.com" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: [Bad Mail]RE: OPT on large molecules
Message-Id: <-30714-060130211934-17396-n27gLqdisGfbGe+aPpAM5Q!=!server.ccl.net>
X-Original-From: Alexander Kollias <ackollias++gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=utf-8
Date: Mon, 30 Jan 2006 21:19:15 -0500
Mime-Version: 1.0


Sent to CCL by: Alexander Kollias [ackollias::gmail.com]
Sam,
	There are several problems in attempting to carry out such calculations
in QMC.  The first problem concerns the calculation of forces in QMC.
This is due to the fact that the force estimator (by Hellmann-Feynman
theorem) has an infinite variance.  Although improved estimators can be
constructed, i.e. using Pulay corrections along with zero-variance
techniques, that will result in a finite variance. Unfortunately these
estimators do not provide sufficient improvement in the variance for
geometry optimization, if the geometry is far from equilibrium. Second
there is the problem of reoptimizing the MOs at each step in the
geometry optimization. Both of these problems are areas of active
research.  To date triatomics (XH2) are the largest molecules for which
the force has be calculated while orbital optimization has some greater
success. Finally, QMC calculations for large systems require hundreds of
thousands of hours.  This is because although the variance of the local
energy decreases as 1/sqrt(T) where T is computer time, the inherent
variance associated with a trial function tends to grow with the
magnitude of the total energy, i.e. the larger the total energy the
larger the initial variance and associated error bar of the local
energy.
regards,
	Sasha

On Mon, 2006-01-30 at 19:47 -0500, Abrash, Samuel sabrash/arichmond.edu
wrote:
> Sent to CCL by: "Abrash, Samuel" [sabrash!=!richmond.edu]
> 
> Could you use quantum monte carlo to do the optimization?
>  
> Sam
> 
>         -----Original Message----- 
>         From: Shobe, David dshobe[#]sud-chemieinc.com [mailto:owner-chemistry() ccl.net] 
>         Sent: Mon 1/30/2006 12:14 PM 
>         To: Abrash, Samuel 
>         Cc: 
>         Subject: CCL: OPT on large molecules
>         
>         
> 
>         Sent to CCL by: "Shobe, David" [dshobe.() .sud-chemieinc.com]
>         We still haven't answered the main question: will the lack of optimization
> significantly effect the intramolecular charge transfer?  I'll assume here that the
> effect in question does not involve vibrational frequencies.
>         
>         Even if the use of an arbitrary geometry doesn't materially change the results of
> the calculation, I would imagine you'd have some trouble convincing peer reviewers
> of that.  But there are some options (besides just being patient :-).
>         
>         1. You could use molecualr mechanics to do the optimization
>         2. You could use an X-ray diffraction or other published structure, if one exists.
>         3. You could repeat the calculation at several geometries to demonstrate that,
> indeed, the calculated results do not have a significant dependence on molecular
> geometry.
>         
>         The idea of checking whether the effect occurs at all, using an arbitrary but
> reasonable geometry, might not be a bad one.  After this investigational
> calculation, you could then decide whetehr it's worthwhile to redo the calculation
> with a proper geometry (and with all the other i's dotted and t's crossed, as it
> were).
>         
>         --David Shobe, Ph.D., M.L.S.
>         Süd-Chemie, Inc.
>         phone (502) 634-7409
>         fax (502) 634-7724
>         
>         Don't bother flaming me: I'm behind a firewall.
>         
>         
>         
>         -----Original Message-----
>         > From: owner-chemistry%a%ccl.net [mailto:owner-chemistry%a%ccl.net]
> 
>         Sent: Saturday, January 28, 2006 3:48 PM
>         To: Shobe, David
>         Subject: CCL: OPT on large molecules
>         
>         Sent to CCL by: "David M. Close" [closed(_)etsu.edu]
>           CCLers:
>           I have a question about the necessity of optimizations.  I have uncovered an
> effect experimentally that involves changes in large molecules.  By large I mean
> that even partial optimizations with modest basis sets take several days.  The
> effect involves charge migration from one region of the molecule to another
> region.  I would like to examine this effect with computations.  After a weeks
> work I still don't have an answer because of the times taken to determine the
> optimized structures.
>           I realize that the correct approach is to do calculations on the optimized
> structures.  For example, it is necessary to do frequency calculations on the
> optimized structures using the same basis sets in both calculations.  But what if
> one didn't use the optimized structures?  Suppose one only used a good guess at
> the optimized structure?  Would this cause the later calculations to be invalid? 
> Or might they be good enough to at least decide if the effect of interest is
> present and that actual optimizations are worthwhile?
>           Regards, Dave Close.
> 
> [Edited by jkl() ccl.net to removed winmail.dat attachment]> 
> 
>