From owner-chemistry@ccl.net Thu Jan 15 04:06:01 2009
From: "Roland H Lindh roland.lindh*_*teokem.lu.se" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: CASPT2 transition metal complex excitation energies
Message-Id: <-38430-090115035408-18565-TNwH5DBcrmT+xZQwPCkzlw .. server.ccl.net>
X-Original-From: "Roland H Lindh" <roland.lindh(~)teokem.lu.se>
Date: Thu, 15 Jan 2009 03:54:04 -0500


Sent to CCL by: "Roland H Lindh" [roland.lindh||teokem.lu.se]
Dear CCL Subscribers,
 I'm calling on you for help. We are currently benchmarking the CASPT2 method for excitation energies. For that purpose we need, in addition to a set of organic molecules, which we already have, also some transition metal complex. If you have any old MOLCAS input decks around from CASPT2 calculations we would be very glad to recycle these. In return we will cite your work whenever we us the test suite in the future.

If this is possible we would like to have:
1. the MOLCAS input deck (the CASSCF and CASPT2 calculations should be in a single input deck,
2. any associated MO vector files,
3. reference values of the excitation energies,
4. the version of MOLCAS which was used in your case and
5. the reference that you would like us to cite.

Thanks for your help and contribution!

Roland Lindh
roland.lindh---teokem.lu.se


From owner-chemistry@ccl.net Thu Jan 15 09:13:01 2009
From: "Francesca Mocci francimocci .. tiscali.it" <owner-chemistry[a]server.ccl.net>
To: CCL
Subject: CCL:G: G03, problem with PCM : ALPHA scaling factor with UAKS not read correctly
Message-Id: <-38431-090114191355-9383-vHw37uiVNlpHiuGnaViDIA[a]server.ccl.net>
X-Original-From: Francesca Mocci <francimocci/a\tiscali.it>
Content-Type: multipart/alternative;
 boundary="------------010106050601080904050104"
Date: Thu, 15 Jan 2009 00:35:10 +0100
MIME-Version: 1.0


Sent to CCL by: Francesca Mocci [francimocci-#-tiscali.it]
This is a multi-part message in MIME format.
--------------010106050601080904050104
Content-Type: text/plain; charset=ISO-8859-15; format=flowed
Content-Transfer-Encoding: 7bit

Hi all,

I'm using g03 revision C02 to  optimize the structure of a molecule 
modeling the solvent through PCM
defining the molecular cavity through the UAKS model
and using an electrostatic scaling factor for the sphere radius of 1.4

This is the input:
> %chk=uaks_1.4_ch3cn_6311gdp.chk
> # pbe1pbe/6-311g(d,p) opt  SCRF=(PCM,Read,Solvent=acetonitrile)
> # freq
>
> 14gen09
>
> 0 1
> coordinates of the system
>
> TABS=298.
> RADII=UAKS
> ALPHA=1.4


But the program seems not to read correctly the ALPHA input, infact in 
the output file
it writes:

> Using the following non-standard input for PCM:
>  TABS=298.
>  RADII=UAKS
>  ALPHA=1.4
>  --- end of non-standard input.
>  ------------------------------------------------------------------------------
>  United Atom Topological Model (UAKS parameters set).
>   Nord Group  Hybr  Charge Alpha Radius          Bonded to
>     1   C     sp2   0.00   1.20  1.680   O2   [s]  O7   [d]  C8   [s]
>     2   O     sp3   0.00   1.20  1.500   C1   [s]  C3   [s]
>     3   CH3   sp3   0.00   1.20  1.950   O2   [s]
>     7   O     sp2   0.00   1.20  1.500   C1   [d]
>     8   CH3   sp3   0.00   1.20  1.950   C1   [s]
>  ------------------------------------------------------------------------------
If the cavity is defined with the UA0 model the ALPHA value is read 
correctly:

>  Using the following non-standard input for PCM:
>  TABS=298.
>  ALPHA=1.4
>  --- end of non-standard input.
>  ------------------------------------------------------------------------------
>  United Atom Topological Model (UA0  parameters set).
>   Nord Group  Hybr  Charge Alpha Radius          Bonded to
>     1   C     *     0.00   1.40  1.925   O2   [s]  O7   [d]  C8   [s]
>     2   O     *     0.00   1.40  1.750   C1   [s]  C3   [s]
>     3   CH3   *     0.00   1.40  2.525   O2   [s]
>     7   O     *     0.00   1.40  1.750   C1   [d]
>     8   CH3   *     0.00   1.40  2.525   C1   [s]
>  ------------------------------------------------------------------------------
Is this a bug or am  I missing something?
Any hint on how to solve this problem would be very welcome!

Best Regards,
Francesca Mocci





  

--------------010106050601080904050104
Content-Type: text/html; charset=ISO-8859-15
Content-Transfer-Encoding: 8bit

<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-15"
 http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi all,<br>
<br>
I'm using g03 revision C02 to  optimize the structure of a molecule
modeling the solvent through PCM<br>
defining the molecular cavity through the UAKS model<br>
and using an electrostatic scaling factor for the sphere radius of 1.4<br>
<br>
This is the input:<br>
<small>
<blockquote type="cite"><big>%chk=uaks_1.4_ch3cn_6311gdp.chk<br>
# pbe1pbe/6-311g(d,p) opt  SCRF=(PCM,Read,Solvent=acetonitrile)<br>
# freq<br>
  <br>
14gen09<br>
  <br>
0 1<br>
coordinates of the system<br>
  <br>
TABS=298.<br>
RADII=UAKS<br>
ALPHA=1.4</big></blockquote>
<br>
<br>
<big>But the program seems not to read correctly the ALPHA input,
infact in the output file <br>
it writes:<br>
<br>
<blockquote type="cite"><small><big><tt>Using the following
non-standard input for PCM:<br>
 TABS=298.<br>
 RADII=UAKS<br>
 ALPHA=1.4<br>
 --- end of non-standard input.<br>
 ------------------------------------------------------------------------------<br>
 United Atom Topological Model (UAKS parameters set).<br>
  Nord Group  Hybr  Charge Alpha Radius          Bonded to<br>
    1   C     sp2   0.00   1.20  1.680   O2   [s]  O7   [d]  C8   [s]<br>
    2   O     sp3   0.00   1.20  1.500   C1   [s]  C3   [s]<br>
    3   CH3   sp3   0.00   1.20  1.950   O2   [s]<br>
    7   O     sp2   0.00   1.20  1.500   C1   [d]<br>
    8   CH3   sp3   0.00   1.20  1.950   C1   [s]</tt><br>
 ------------------------------------------------------------------------------</big></small></blockquote>
If the cavity is defined with the UA0 model the ALPHA value is read
correctly:<br>
<br>
<blockquote type="cite"><tt> Using the following non-standard input for
PCM:<br>
 TABS=298.<br>
 ALPHA=1.4<br>
 --- end of non-standard input.<br>
 ------------------------------------------------------------------------------<br>
 United Atom Topological Model (UA0  parameters set).<br>
  Nord Group  Hybr  Charge Alpha Radius          Bonded to<br>
    1   C     *     0.00   1.40  1.925   O2   [s]  O7   [d]  C8   [s]<br>
    2   O     *     0.00   1.40  1.750   C1   [s]  C3   [s]<br>
    3   CH3   *     0.00   1.40  2.525   O2   [s]<br>
    7   O     *     0.00   1.40  1.750   C1   [d]<br>
    8   CH3   *     0.00   1.40  2.525   C1   [s]<br>
 ------------------------------------------------------------------------------<br>
  </tt></blockquote>
Is this a bug or am </big></small><small><big> I </big></small><small><big>
missing something?<br>
Any hint on how to solve this problem would be very welcome!<br>
<br>
Best Regards,<br>
Francesca Mocci<br>
<br>
<br>
</big></small><br>
<br>
<br>
   <br>
</body>
</html>

--------------010106050601080904050104--


From owner-chemistry@ccl.net Thu Jan 15 12:28:01 2009
From: "Richard Tia richtiagh(_)gmail.com" <owner-chemistry]=[server.ccl.net>
To: CCL
Subject: CCL: Re-submitting a previously 'killed' job in spartan
Message-Id: <-38432-090115122626-10331-iCUxmN921Xxj5dK/QEy18Q]=[server.ccl.net>
X-Original-From: "Richard  Tia" <richtiagh(0)gmail.com>
Date: Thu, 15 Jan 2009 12:26:23 -0500


Sent to CCL by: "Richard  Tia" [richtiagh(-)gmail.com]
Hi everybody,
Please forgive me if my question sounds trivial but I'm new to spartan.
If I had to kill a job on spartan '06 for some reason, can I get it to start from where it left off when I re-submit later or it will have to start all over again(from scratch).

Thanks in advance for your assistance.

Richard Tia
KNUST, Kumasi
Ghana
richtiagh()gmail.com


From owner-chemistry@ccl.net Thu Jan 15 13:03:01 2009
From: "Rachelle Joyce Bienstock biensto1#niehs.nih.gov" <owner-chemistry(!)server.ccl.net>
To: CCL
Subject: CCL: Recommendations for computer hardware
Message-Id: <-38433-090114134548-9507-OLfRVEHICHvqUaqqvdvRCA(!)server.ccl.net>
X-Original-From: "Rachelle Joyce Bienstock" <biensto1-*-niehs.nih.gov>
Date: Wed, 14 Jan 2009 13:45:44 -0500


Sent to CCL by: "Rachelle Joyce Bienstock" [biensto1(-)niehs.nih.gov]


I am looking to purchase a new machine to run AMBER, CHARMm,
NAMD, Accelrys and Schrodinger software.

What would be your recommendations for a machine for optimum 
performance for these applications and this use (modeling,
visualization and simulation):

Processor: Intel Core Duo, 2 Duo, 2Quad, 2Extreme??

How many processors?  Can the Schrodinger and
Accelrys software take advantage of and use multiple
processors of this kind?  how many? are there particular processors their software is optimized for?

32 bit or 64 bit Linux?  
How much memory is sufficient?

What about stereo?  Are there Linux Centos 5 drivers that support Open GL stereo graphics with Nvidia Quadro FX cards?


From owner-chemistry@ccl.net Thu Jan 15 13:38:00 2009
From: "Mohamed Abdulhameed mabdu3+/-email.uky.edu" <owner-chemistry^^^server.ccl.net>
To: CCL
Subject: CCL: clustering docked poses
Message-Id: <-38434-090115130824-31813-MQwEw5E67ds5F8ifYeK1aA^^^server.ccl.net>
X-Original-From: "Mohamed  Abdulhameed" <mabdu3^-^email.uky.edu>
Date: Thu, 15 Jan 2009 13:08:20 -0500


Sent to CCL by: "Mohamed  Abdulhameed" [mabdu3:+:email.uky.edu]
Hello everyone,

I had docked some 80 ligands to my target protein and got 100 docked poses for each ligand. I would like to cluster the poses (based on RMSD). I think this will help me to quickly select the more distinct poses. 

It will be helpful if anyone can tell me how I can do the clustering of poses. Is there any free software to do this? It will also be helpful if anyone can point out some links/websites towards clustering of compounds. 

Thank you for your time.

regards,
Mohamed Diwan 
Graduate student
College of Pharmacy
University of Kentucky


From owner-chemistry@ccl.net Thu Jan 15 15:58:00 2009
From: "Kyle Beran beran_k*utpb.edu" <owner-chemistry*_*server.ccl.net>
To: CCL
Subject: CCL: Re-submitting a previously 'killed' job in spartan
Message-Id: <-38435-090115153136-4861-MJHR9TE2ze2CdY2EbeVBug*_*server.ccl.net>
X-Original-From: "Kyle Beran" <beran_k{=}utpb.edu>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain;
	charset="us-ascii"
Date: Thu, 15 Jan 2009 13:58:52 -0600
MIME-Version: 1.0


Sent to CCL by: "Kyle Beran" [beran_k(_)utpb.edu]
Richard

I've used various versions of Spartan for ~8 years.  Sorry, but it will have
to start over from scratch (or, I've never read anything to the effect of
re-starting a calculation from the point at which it was killed).

Regards,
Kyle

-----Original Message-----
> From: owner-chemistry+beran_k==utpb.edu,+,ccl.net
[mailto:owner-chemistry+beran_k==utpb.edu,+,ccl.net] On Behalf Of Richard Tia
richtiagh(_)gmail.com
Sent: Thursday, January 15, 2009 11:26 AM
To: Beran, Kyle 
Subject: CCL: Re-submitting a previously 'killed' job in spartan


Sent to CCL by: "Richard  Tia" [richtiagh(-)gmail.com]
Hi everybody,
Please forgive me if my question sounds trivial but I'm new to spartan.
If I had to kill a job on spartan '06 for some reason, can I get it to start
> from where it left off when I re-submit later or it will have to start all
over again(from scratch).

Thanks in advance for your assistance.

Richard Tia
KNUST, Kumasi
Ghana
richtiagh,,gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt

From owner-chemistry@ccl.net Thu Jan 15 22:55:00 2009
From: "David Gallagher gallagher.da_+_gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Modelling whole proteins with quantum chemistry
Message-Id: <-38436-090115224255-9861-DhvkCYMZPYuc+pChcLNVDw#,#server.ccl.net>
X-Original-From: David Gallagher <gallagher.da/./gmail.com>
Content-Type: multipart/alternative;
	boundary="=====================_46162140==.ALT"
Date: Thu, 15 Jan 2009 18:42:39 -0800
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da[*]gmail.com]
--=====================_46162140==.ALT
Content-Type: text/plain; charset="us-ascii"; format=flowed

Modelling whole proteins with quantum chemistry

A review on the modelling of whole proteins including metalloenzymes, 
using the new PM6 semiempirical method and linear scaling algorithm 
(Mozyme) in MOPAC2009 has just been published in the Journal of 
Molecular Modelling.

The review includes numerous examples, including a simple enzyme 
reaction coordinate, salt-bridges, ion channels, comparisons with 
other computational methods and X-ray crystal structures, and 
discussions on the advantages and limitations.

The link to the full text, "Application of the PM6 method to modeling 
proteins", is at
http://www.cacheresearch.com/mopac.html#mopac-support (at the end of 
the MOPAC bibliography).

MOPAC2009, released in November 2008, is available free to academics.

Enjoy,
David Gallagher
CACheResearch.com  
--=====================_46162140==.ALT
Content-Type: text/html; charset="us-ascii"

<html>
<body>
<b>Modelling whole proteins with quantum chemistry<br><br>
</b>A review on the modelling of whole proteins including metalloenzymes,
using the new PM6 semiempirical method and linear scaling algorithm
(Mozyme) in MOPAC2009 has just been published in the Journal of Molecular
Modelling.<br><br>
The review includes numerous examples, including a simple enzyme reaction
coordinate, salt-bridges, ion channels, comparisons with other
computational methods and X-ray crystal structures, and discussions on
the advantages and limitations.&nbsp; <br><br>
The link to the full text, &quot;<font color="#131413">Application of the
PM6 method to modeling proteins</font>&quot;, is at<br>
<a href="http://www.cacheresearch.com/mopac.html#mopac-support" eudora="autourl">
http://www.cacheresearch.com/mopac.html#mopac-support</a> (at the end of
the MOPAC bibliography). <br><br>
MOPAC2009, released in November 2008, is available free to
academics.<br><br>
Enjoy,<br>
David Gallagher<br>
CACheResearch.com </body>
</html>

--=====================_46162140==.ALT--