From owner-chemistry@ccl.net Sat Aug 23 02:45:01 2008
From: "Mr shabbir shabbir===nenu.edu.cn" <owner-chemistry=-=server.ccl.net>
To: CCL
Subject: CCL: Error in Mp2 calculation
Message-Id: <-37601-080823022530-16605-NqlLObDbIs3EQwL/8R3y5Q=-=server.ccl.net>
X-Original-From: "Mr  shabbir" <shabbir()nenu.edu.cn>
Date: Sat, 23 Aug 2008 02:25:21 -0400


Sent to CCL by: "Mr  shabbir" [shabbir#nenu.edu.cn]
Hi 
I also faced such problem then used %Mem=3Gb with a bigger machine it would ok try that...
Regards

Mr.Shabbir


> "Mousumi Bezbora Phukan mousumiphukan]_[gmail.com"  wrote:
> 
> Sent to CCL by: "Mousumi Bezbora Phukan" [mousumiphukan__gmail.com]
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> 
> Dear All,
> 
> I was trying to run a MP2/6-31+G* calculation for a system with 232
> basis functions using the following route card:
> 
> #mp2(maxdisk=40GB)/6-31+g* fopt freq geom=check guess=read
> 
> Before starting the calculation, I checked the disk space and found
> that 55GB is available.
> 
> Filesystem            Size  Used  Avail Use%    Mounted on
> /dev/mapper/VolGroup00-LogVol00
>                             73G   14G   55G  21%         /
> /dev/sda1              99M   12M   82M 13%        /boot
> none                  247M     0     247M   0%         /dev/shm
> 
> However, after running the calculation, I got the following message.
> 
>  **** Warning!!: The largest alpha MO coefficient is  0.60503943D+02
> 
>  Disk-based method using ON**2 memory for 30 occupieds at a time.
>  Estimated scratch disk usage=   594240712 words.
>  Actual    scratch disk usage=   593732296 words.
> Erroneous write during file extend. write 28671 instead of 4096
> Probably out of disk space.
> Write error in NtrExt1: Success
> Erroneous write during file extend. write 28671 instead of 4096
> Probably out of disk space.
> Write error in NtrExt1
> 
> But, when I checked the disk space again, the available space was still 53GB.
> 
> I shall be very much obliged if some one can help me out.
> 
> Regards,
> 
> M. B. Phukan
> 
> ------=_Part_7503_11806460.1219224243622
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> 
> <div dir="ltr"><pre style="font-family: comic sans ms,sans-serif;"><font style="font-family: arial,helvetica,sans-serif;" size="2">Dear All,<br><br>I was trying to run a MP2/6-31+G* calculation for a system with 232 basis functions using the following route card:<br>
> <br>#mp2(maxdisk=40GB)/6-31+g* fopt freq geom=check guess=read<br><br>Before starting the calculation, I checked the disk space and found that 55GB is available.<br><br>Filesystem            Size  Used  Avail Use%    Mounted on<br>
> /dev/mapper/VolGroup00-LogVol00<br>                            73G   14G   55G  21%         /<br>/dev/sda1              99M   12M   82M 13%        /boot<br>none                  247M     0     247M   0%         /dev/shm  <br>
> <br>However, after running the calculation, I got the following message.<br><br> **** Warning!!: The largest alpha MO coefficient is  0.60503943D+02<br><br> Disk-based method using ON**2 memory for 30 occupieds at a time.<br>
>  Estimated scratch disk usage=   594240712 words.<br> Actual    scratch disk usage=   593732296 words.<br>Erroneous write during file extend. write 28671 instead of 4096<br>Probably out of disk space.<br>Write error in NtrExt1: Success<br>
> Erroneous write during file extend. write 28671 instead of 4096<br>Probably out of disk space.<br>Write error in NtrExt1                    <br><br>But, when I checked the disk space again, the available space was still 53GB.<br>
> <br>I shall be very much obliged if some one can help me out.<br><br>Regards,<br></font><br>M. B. Phukan<br></pre></div>
> 
> ------=_Part_7503_11806460.1219224243622--
> 
>


From owner-chemistry@ccl.net Sat Aug 23 07:08:01 2008
From: "Syed Tarique Moin tarisyed###yahoo.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Copper
Message-Id: <-37602-080823070217-20423-aJ3b1Kzn/JWkWMhslnYQwA##server.ccl.net>
X-Original-From: "Syed Tarique Moin" <tarisyed]=[yahoo.com>
Date: Sat, 23 Aug 2008 07:02:14 -0400


Sent to CCL by: "Syed Tarique Moin" [tarisyed\a/yahoo.com]
Hello,

We are working on a metalloprotein containing two copper ion (in its +2 oxidation state)  in the active site. Each copper is tighly coordinated in square planar geometry to both atoms of the oxygen molecule and to epsilon N atoms of two of the three histidine ligands. These two copper, two oxgen and four epsilon N atoms approximately form a single plane. Above and below this the epsilon nitrogen of two histidine complete the coordination spheres of these two coppers by occupying more distal axial square pyramidal postions. We want to carry ESP calculation for this coordination system by mean Quantum Software. We require the ionic radius of copper in this penta coordinate geometry.

We have radius for the other coordination system as given below.
Ion                     coordination type                 Radius/pm
Cu(I)             4-coordinate, tetrahedral                  74
Cu(II)            4-coordinate, tetrahedral                  71
Cu(II)            4-coordinate, square-planar                71
Cu(I)             6-coordinate, octahedral                   91
Cu(II)            6-coordinate, octahedral                   87
Cu(III)           6-coordinate, octahedral                   68

But we require radius for copper (II), 5-coordinate, square pyramidal and we didn't get this information by any means.
This is our prime requirement for the ESP Calculation.
Can any give idea about it. 

Regards


From owner-chemistry@ccl.net Sat Aug 23 07:42:00 2008
From: "Alcides Simao alsimao(-)gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL:G: Error in Mp2 calculation
Message-Id: <-37603-080823071915-25722-cRue/Spwt96EjQjN31wUyA(-)server.ccl.net>
X-Original-From: "Alcides Simao" <alsimao,gmail.com>
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Date: Sat, 23 Aug 2008 12:19:04 +0100
MIME-Version: 1.0


Sent to CCL by: "Alcides Simao" [alsimao:gmail.com]
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Mr Shabbir,

%mem %rwf are different, but interconnected, concepts!
If you allocate every bit of info in your RAM, you'll find yourself quickly
without RAM. The main purpose of the scratch files is to prevent that. Data
is dynamically allocated in the RAM, enhancing speed of your calculation,
and enabling you to execute jobs that otherwise would be impossible to be
executed directly in the RAM. The maximum amount of rwf allowed by GAUSSIAN
by default is 8 x 250 MW. a typical syntax would be:

%rwf=a,250mw,b,250mw,c,250mw,d,250mw,e,250mw,f,250mw,g,250mw,h,250mw

This syntax allows you to use %rwf to its maximum. %rwf is written on the
SCRATCH directoty in the GAUSSIAN directory.

I hope that this helps you!

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<div dir="ltr">Mr Shabbir,<br><br>%mem %rwf are different, but interconnected, concepts!<br>If you allocate every bit of info in your RAM, you&#39;ll find yourself quickly without RAM. The main purpose of the scratch files is to prevent that. Data is dynamically allocated in the RAM, enhancing speed of your calculation, and enabling you to execute jobs that otherwise would be impossible to be executed directly in the RAM. The maximum amount of rwf allowed by GAUSSIAN by default is 8 x 250 MW. a typical syntax would be:<br>
<br>%rwf=a,250mw,b,250mw,c,250mw,d,250mw,e,250mw,f,250mw,g,250mw,h,250mw<br><br>This syntax allows you to use %rwf to its maximum. %rwf is written on the SCRATCH directoty in the GAUSSIAN directory.<br><br>I hope that this helps you!<br>
</div>

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From owner-chemistry@ccl.net Sat Aug 23 11:35:00 2008
From: "Brian Williams williams]=[bucknell.edu" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL:G: Determining whether a transition is n-pi* or pi-pi*
Message-Id: <-37604-080822125646-29006-y5b7V/ULBD9myz8aGrzN/g|server.ccl.net>
X-Original-From: Brian Williams <williams_+_bucknell.edu>
Content-Type: multipart/alternative; 
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Date: Fri, 22 Aug 2008 12:12:00 -0400 (EDT)
MIME-Version: 1.0


Sent to CCL by: Brian Williams [williams]=[bucknell.edu]

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Dear Matthew: 

I don't know that the way I approach this problem is the most efficient, but what I usually do to get a sense of this is to actually plot the MO's involved in the transition and look to see if they have pi or n character. Usually, it is obvious, in that orbitals with n character have wavefunction density in planes perpindicular to those with pi character, and are also associated with atoms you would expect to have lone pairs. I'm more used to doing this with CI based calculations, where you have to look at all the transitions involved; I always have found that the patterns hold for all the orbitals involved in any particular transition. 

Experimentally, you can also often try to decide on n-pi * or pi-pi* based on how the spectral bands shift with solvent polarity. Pi-pi* often go red with increased polarity, while n-pi* go blue. This is described in many places-the reference I have to hand for this is Parker, " Photoluminescence of Solutions", 1968. 

Hope this is of use. 

Brian Williams, Chemistry 
Bucknell University 


----- Original Message ----- 
> From: "Matthew K Morantz matthew.morantz{}gmail.com" <owner-chemistry*ccl.net> 
To: "Brian  Williams" <williams*bucknell.edu> 
Sent: Friday, August 22, 2008 4:52:53 AM GMT -05:00 US/Canada Eastern 
Subject: CCL:G: Determining whether a transition is n-pi* or pi-pi* 


Sent to CCL by: "Matthew K Morantz" [matthew.morantz-.-gmail.com] 
Hi, 

Just a quick and simple question: 

I've optimized a D2h-symmetry molecule at the DFT-B3LYP-6/31G level of theory in Gaussian. I've figured out the HOMO-LUMO gap from the orbital energies. 
I'm now attempting to correlate this gap with the experimental max of the molecule. 
I know that E(HOMO-LUMO) = E(lambdamax) = hv and have calculated E(max)experimental and E(lambdamax)theoretical as a result. 

However, E(lambdamax)exp > E(lambdamax)theo and I want to check whether solvation effects could be expected to cause a red- or blue-shift. For this, I need to know whether the b1g --> b3u transition at max is n-->pi* or pi-->pi*. 

How do I go about figuring that out from my calculations? 

Thanks, 

Matthew Morantz 
matthew.morantz:+:gmail.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt------=_Part_56727_425586888.1219421520911
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<html><head><style type=3D'text/css'>p { margin: 0; }</style></head><body><=
div style=3D'font-family: Times New Roman; font-size: 12pt; color: #000000'=
>Dear Matthew:<br>
<br>
I don't know that the way I approach this problem is the most
efficient, but what I usually do to get a sense of this is to actually
plot the MO's involved in the transition and look to see if they have
pi or n character.&nbsp; Usually, it is obvious, in that orbitals with
n character have wavefunction density in planes perpindicular to those
with pi character, and are also associated with atoms you would expect
to have lone pairs.&nbsp; I'm more used to doing this with CI based
calculations, where you have to look at all the transitions involved; I
always have found that the patterns hold for all the orbitals involved
in any particular transition.<br>
<br>
Experimentally, you can also often try to decide on n-pi * or pi-pi*
based on how the spectral bands shift with solvent polarity.&nbsp;
Pi-pi* often go red with increased polarity, while n-pi* go blue.&nbsp;
This is described in many places-the reference I have to hand for this
is Parker, " Photoluminescence of Solutions", 1968. <br>
<br>
Hope this is of use.<br>
<br>
Brian Williams, Chemistry<br>
Bucknell University<br>
<br>
<br>----- Original Message -----<br>From: "Matthew K Morantz matthew.morant=
z{}gmail.com" &lt;owner-chemistry*ccl.net&gt;<br>To: "Brian  Willia=
ms" &lt;williams*bucknell.edu&gt;<br>Sent: Friday, August 22, 2008 4:52:53 =
AM GMT -05:00 US/Canada Eastern<br>Subject: CCL:G: Determining whether a tr=
ansition is n-pi* or pi-pi*<br><br><br>Sent to CCL by: "Matthew K Morantz" =
[matthew.morantz-.-gmail.com]<br>Hi,<br><br>Just a quick and simple questio=
n:<br><br>I've
optimized a D2h-symmetry molecule at the DFT-B3LYP-6/31G level of
theory in Gaussian. I've figured out the HOMO-LUMO gap from the orbital
energies.<br>I'm now attempting to correlate this gap with the experimental=
 max of the molecule.<br>I know that E(HOMO-LUMO) =3D E(lambdamax) =3D hv a=
nd have calculated E(max)experimental and E(lambdamax)theoretical as a resu=
lt.<br><br>However,
E(lambdamax)exp &gt; E(lambdamax)theo and I want to check whether
solvation effects could be expected to cause a red- or blue-shift. For
this, I need to know whether the b1g --&gt; b3u transition at max is
n--&gt;pi* or pi--&gt;pi*.<br><br>How do I go about figuring that out from =
my calculations? <br><br>Thanks,<br><br>Matthew Morantz<br>matthew.morantz:=
+:gmail.com<br><br><br><br>-=3D This is automatically added to each message=
 by the mailing script =3D-<br>To recover the email address of the author o=
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From owner-chemistry@ccl.net Sat Aug 23 19:53:01 2008
From: "Brian Salter-Duke brian.james.duke]-[gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: Error in Mp2 calculation
Message-Id: <-37605-080823191022-17001-tMzFEfjrpd8pX5/cyyFrpg,+,server.ccl.net>
X-Original-From: Brian Salter-Duke <brian.james.duke{=}gmail.com>
Content-Transfer-Encoding: 7bit
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Date: Sun, 24 Aug 2008 08:10:38 +1000
MIME-Version: 1.0


Sent to CCL by: Brian Salter-Duke [brian.james.duke:-:gmail.com]
Alcides Simao alsimao(-)gmail.com wrote:
> Mr Shabbir,
> 
> %mem %rwf are different, but interconnected, concepts!
> If you allocate every bit of info in your RAM, you'll find yourself 
> quickly without RAM. The main purpose of the scratch files is to prevent 
> that. Data is dynamically allocated in the RAM, enhancing speed of your 
> calculation, and enabling you to execute jobs that otherwise would be 
> impossible to be executed directly in the RAM. The maximum amount of rwf 
> allowed by GAUSSIAN by default is 8 x 250 MW. a typical syntax would be:
> 
> %rwf=a,250mw,b,250mw,c,250mw,d,250mw,e,250mw,f,250mw,g,250mw,h,250mw
> 
> This syntax allows you to use %rwf to its maximum. %rwf is written on 
> the SCRATCH directoty in the GAUSSIAN directory.
> 
> I hope that this helps you!

This only applies to 32 bit compiles. 64 bit is not so restrictive.

Brian.


From owner-chemistry@ccl.net Sat Aug 23 21:07:00 2008
From: "Sandeep Kumar Rambhajo%x%gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Bioinformatics software for protein digestion prediction
Message-Id: <-37606-080823204210-8584-Zbt/rYkIoXpbperNZJy7bQ]_[server.ccl.net>
X-Original-From: "Sandeep  Kumar" <Rambhajo ~ gmail.com>
Date: Sat, 23 Aug 2008 20:42:06 -0400


Sent to CCL by: "Sandeep  Kumar" [Rambhajo|-|gmail.com]

Dear All, 

I was wondering if somebody knows about a free bioinformatics software that can  identify potential proteolytic sites for all known proteases in a given protein sequence. A software that uses protein structures to do this job would be simply awesome!

Many thanks in advance. 

Best regards, 
Sandeep Kumar, Ph.D. 
Pfizer Global Biologics, 
St. Louis, MO.