From owner-chemistry@ccl.net Wed Aug 20 02:59:00 2008
From: "Dr.Wolfgang Quapp quapp\a/rz.uni-leipzig.de" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Transition State question
Message-Id: <-37581-080819063654-20846-QC0C/v7tn3S2AwXa3ct9Jw%a%server.ccl.net>
X-Original-From: "Dr.Wolfgang Quapp" <quapp-x-rz.uni-leipzig.de>
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Date: Tue, 19 Aug 2008 11:43:27 +0200
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Sent to CCL by: "Dr.Wolfgang Quapp" [quapp-x-rz.uni-leipzig.de]
Zitat von "Mark Zottola mzottola^^gmail.com" <owner-chemistry*ccl.net>:

> In examining a potential energy surface of a species of interest, I have
> come across something unique to my experience.  I have, apparently, run
> across a system which an intermediate connects to a transition state via
> *another* transition state.  The IRC calculations validate this connection=
.
> The second transition state connects two other species.  In other words
>
> A ---->   B (TS_1) -----> C (TS_2) ;
>
> D ----> C (TS_2) -----> F
>
> The second TS (TS_2)  is a first order saddle point.  Has anyone run acros=
s
> this before?  Or am I missing something fundamental in these calculations?
> I have come across a Schlegel reference where a transition state connects
> three different species.  Yet this communication was for an open-shell
> system.
>
> Thanks for any helpful comments, references, etc.
>
>
> Mark
>

Hallo Mark,

see, for example, model surfaces for your problem in:

Theoret Chem Acc 112 (2004) 40-51,  or
J Molec struct 695-696 (2004) 95-101

Greetings
Dr.Wolfgang Quapp


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From owner-chemistry@ccl.net Wed Aug 20 09:15:01 2008
From: "Mousumi Bezbora Phukan mousumiphukan]_[gmail.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: Error in Mp2 calculation
Message-Id: <-37582-080820074836-21187-ZdXMSSfp7aPmcudTjUCBFg!^!server.ccl.net>
X-Original-From: "Mousumi Bezbora Phukan" <mousumiphukan,+,gmail.com>
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Date: Wed, 20 Aug 2008 14:54:02 +0530
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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

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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>

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From owner-chemistry@ccl.net Wed Aug 20 09:51:01 2008
From: "Ashwini Phukan ashwini_phukan=yahoo.com" <owner-chemistry^_^server.ccl.net>
To: CCL
Subject: CCL: MP2 calculation
Message-Id: <-37583-080820050014-5780-VBCIwZFl8bdCgjoAtKMZsA^_^server.ccl.net>
X-Original-From: Ashwini Phukan <ashwini_phukan,,yahoo.com>
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Date: Wed, 20 Aug 2008 00:59:59 -0700 (PDT)
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Sent to CCL by: Ashwini Phukan [ashwini_phukan{}yahoo.com]
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,

A. K. Phukan


From owner-chemistry@ccl.net Wed Aug 20 10:26:00 2008
From: "Yonggang Yang ygyang__chemie.fu-berlin.de" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL:G: hermiticity of the one electron integral matrix
Message-Id: <-37584-080820055941-10624-B86S2//H1WHzFDNfxZFKRQ,,server.ccl.net>
X-Original-From: Yonggang Yang <ygyang|*|chemie.fu-berlin.de>
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Date: Wed, 20 Aug 2008 11:26:09 +0200
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Sent to CCL by: Yonggang Yang [ygyang=chemie.fu-berlin.de]
The equation is not correct for arbitrary functions. But it is correct
for any functions in the Hilbert space--square integrable functions. In
a simple way the function value should go to zero when one of the
coordinate is infinity. 

On Tue, 2008-08-19 at 06:42 -0400, Shuwen yao lilichemistry]~[yahoo.com
wrote:
> Sent to CCL by: "Shuwen  yao" [lilichemistry**yahoo.com]
> As is well known, the kinetic or potential energy matrix of one electron integral on the gaussian output is a symmetric one, which may be rationalized by the hermiticity of the operator. But I really can not understand it mathematically,say, for any two different functions f1 and f2,i doubt the following quation holds always 
>                  interal of f1*d/d2(f2)=integral of f2*d/d2(f1)
> it will be appreciated very much if you could show me a way out> 
>


From owner-chemistry@ccl.net Wed Aug 20 11:00:00 2008
From: "Close, David M. CLOSED^_^mail.etsu.edu" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL:G: Error in Mp2 calculation
Message-Id: <-37585-080820101336-32211-4HyiBXQ1PrwhYvvtq2TXoQ .. server.ccl.net>
X-Original-From: "Close, David M." <CLOSED^mail.etsu.edu>
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Sent to CCL by: "Close, David M." [CLOSED a mail.etsu.edu]
This is a multi-part message in MIME format.

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This problem comes up on the CCL about once a month.  First you have to
tell us what program you are using, and what computer you are using.
Commonly this questions comes up with Gaussian users on 32 bit machines.
I am guessing from your #mp2 keyword line that you are using Gaussian?
If so there are limitations in writing scratch files.  The limitations
involve how many addresses the CPU can write.  For example a 32 bit
machine can write 16gB unique addresses.  Gaussian typically write these
in 2gB files, as described in the manual under rwf.x.  So looking at the
available disk space doesn't help in this case. =20

=20

> From: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net]=20
Sent: Wednesday, August 20, 2008 5:24 AM
To: Close, David M.
Subject: CCL: Error in Mp2 calculation

=20

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=3D40GB)/6-31+g* fopt freq geom=3Dcheck guess=3Dread



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 =20






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=3D   594240712 words.

 Actual    scratch disk usage=3D   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                   =20



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

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<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>This problem comes up on the CCL about once a =
month.&nbsp; First
you have to tell us what program you are using, and what computer you =
are
using.&nbsp; Commonly this questions comes up with Gaussian users on 32 =
bit
machines.&nbsp; I am guessing from your #mp2 keyword line that you are =
using
Gaussian?&nbsp; If so there are limitations in writing scratch =
files.&nbsp; The
limitations involve how many addresses the CPU can write.&nbsp; For =
example a
32 bit machine can write 16gB unique addresses.&nbsp; Gaussian typically =
write
these in 2gB files, as described in the manual under rwf.x.&nbsp; So =
looking at
the available disk space doesn&#8217;t help in this case.&nbsp; =
<o:p></o:p></span></p>

<p class=3DMsoNormal><span =
style=3D'font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p>&nbsp;</o:p></span></p>

<div style=3D'border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt =
0in 0in 0in'>

<p class=3DMsoNormal><b><span =
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span>=
</b><span
style=3D'font-size:10.0pt;font-family:"Tahoma","sans-serif"'> =
owner-chemistry(a)ccl.net
[mailto:owner-chemistry(a)ccl.net] <br>
<b>Sent:</b> Wednesday, August 20, 2008 5:24 AM<br>
<b>To:</b> Close, David M.<br>
<b>Subject:</b> CCL: Error in Mp2 calculation<o:p></o:p></span></p>

</div>

<p class=3DMsoNormal><o:p>&nbsp;</o:p></p>

<div><pre><span style=3D'font-family:"Arial","sans-serif"'>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>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'><br>
#mp2(maxdisk=3D40GB)/6-31+g* fopt freq geom=3Dcheck guess=3Dread<br>
<br>
Before starting the calculation, I checked the disk space and found that =
55GB is available.<br>
<br>
Filesystem&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp; Size&nbsp; Used&nbsp; Avail Use%&nbsp;&nbsp;&nbsp; Mounted on<br>
<br>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'>/dev/mapper/VolGroup00-LogVol0=
0<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&=
nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp; 73G&nbsp;&nbsp; 14G&nbsp;&nbsp; 55G&nbsp; =
21%&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /<br>
/dev/sda1&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;99M&nbs=
p;&nbsp; 12M&nbsp;&nbsp; 82M =
13%&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /boot<br>
none&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 247M&nbsp;&nbsp;&nbsp;&nbsp; =
0&nbsp;&nbsp;&nbsp;&nbsp; 247M&nbsp;&nbsp; =
0%&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; /dev/shm&nbsp; <br>
<br>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'><br>
However, after running the calculation, I got the following message.<br>
<br>
&nbsp;**** Warning!!: The largest alpha MO coefficient is&nbsp; =
0.60503943D+02<br>
<br>
&nbsp;Disk-based method using ON**2 memory for 30 occupieds at a =
time.<br>
<br>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'>&nbsp;Estimated scratch disk =
usage=3D&nbsp;&nbsp; 594240712 words.<br>
&nbsp;Actual&nbsp;&nbsp;&nbsp; scratch disk usage=3D&nbsp;&nbsp; =
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>
<br>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'>Erroneous write during file =
extend. write 28671 instead of 4096<br>
Probably out of disk space.<br>
Write error in =
NtrExt1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <br>
<br>
But, when I checked the disk space again, the available space was still =
53GB.<br>
<br>
<o:p></o:p></span></pre><pre><span =
style=3D'font-family:"Arial","sans-serif"'><br>
I shall be very much obliged if some one can help me out.<br>
<br>
Regards,<br>
</span><span style=3D'font-family:"Comic Sans MS"'><br>
M. B. Phukan<o:p></o:p></span></pre></div>

</div>

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From owner-chemistry@ccl.net Wed Aug 20 11:40:00 2008
From: "Hemant Srivastava hemantkrsri- -gmail.com" <owner-chemistry**server.ccl.net>
To: CCL
Subject: CCL: Error in Mp2 calculation
Message-Id: <-37586-080820101734-3666-QTSK6M3f/1F8NgNs+FMNPg**server.ccl.net>
X-Original-From: "Hemant Srivastava" <hemantkrsri],[gmail.com>
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Date: Wed, 20 Aug 2008 17:17:22 +0300
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Sent to CCL by: "Hemant Srivastava" [hemantkrsri!^!gmail.com]
Hi,

How much memory you are using?
You may increase it and I think it will help.
You can try %Mem=240MW

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


On 8/20/08, Mousumi Bezbora Phukan mousumiphukan]_[gmail.com
<owner-chemistry]^[ccl.net> wrote:
> 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
>
>


From owner-chemistry@ccl.net Wed Aug 20 12:10:01 2008
From: "Andrew Orry orry.molsoft|,|gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: Protein Structure and Drug Design Workshop - MolSoft October 2-3 2008
Message-Id: <-37587-080818201334-24709-GGoKle6ScL/KW7ArZtvDRA(-)server.ccl.net>
X-Original-From: Andrew Orry <orry.molsoft!A!gmail.com>
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Date: Mon, 18 Aug 2008 16:19:31 -0700
MIME-Version: 1.0


Sent to CCL by: Andrew Orry [orry.molsoft],[gmail.com]

MolSoft ICM Workshop: "Protein Structure and Drug Discovery" October 2nd
to 3rd 2008 La Jolla, CA.

Please see the following invitation to attend MolSoft's
(www.molsoft.com) Protein Structure and Drug Design Workshop on October
2nd to 3rd 2008 in  La Jolla, California USA. See
www.molsoft.com/training.html for more information and a registration form.

Our workshops are suitable for chemists and biologists who would like to
learn more about computational drug discovery and bioinformatics. No
prior knowledge in this field is required to participate. The workshop
is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and
Dr. Maxim Totrov (MolSoft).

The workshops will consist of lectures, demonstrations, and "hands-on"
computational experiments and will cover the following topics:

- Sequence and Protein Structure Analysis
- Protein Modeling and Simulations
- Structure Validation and Optimization
- Ligand Binding Site Prediction
- Small Molecule Docking and Virtual Ligand Screening
- Structure-based development of target-specific compound libraries
- Cheminformatics, chemical clustering, searching, superposition etc
- QSAR, machine learning
- Protein-Protein Docking

We will demonstrate and train you in the use of many of our new
developments in computational chemistry and biology including:

- 3D Ligand Editor - design and optimize ligands interactively
- Markush Library Docking
- Multiple Receptor Docking (A method to incorporate receptor flexibility)
- Automated model building into electron density
- Atomic property field chemical superposition
- Fast machine learning tools for QSAR
- Pharmacophore drawing and searching
- Compound library enumeration tools
- Screen-grabbing movie making

"The objective of this training workshop is to help chemists and
biologists solve challenging problems in the area of drug discovery by
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From owner-chemistry@ccl.net Wed Aug 20 13:41:00 2008
From: "Bernd Wendt bwendt]~[tripos.com" <owner-chemistry##server.ccl.net>
To: CCL
Subject: CCL: Scaffolds for CoMFA contour plots
Message-Id: <-37588-080820133935-17039-Nhfj0TOPKwmJ37usGVcJzQ##server.ccl.net>
X-Original-From: "Bernd  Wendt" <bwendt[-]tripos.com>
Date: Wed, 20 Aug 2008 13:39:31 -0400


Sent to CCL by: "Bernd  Wendt" [bwendt]*[tripos.com]
Dear DD and Deepa,

the Optimize QSAR only works with R-groups or sidechains, i.e. fragments
with only one open valence. I guess by scaffolds you mean core structures
with 2 or more variable R-groups attached. In this case Optimize QSAR would
not be of any help. There are tables with such scaffolds to be found in the
SYBYL tree, i.e. $TA_ROOT/demo/linux/sub2v.tbl or sub3v.tbl that you might
want to try, but I would try another approach. Since you don't want to get
too far away from the scaffolds of your training set, why don't you try the
scaffold search option of the topomeric search tool in SYBYL. Given a
scaffold-query, i.e any 2D-structure of a fragment with 2 or more open 
valences as input, you can search full-structure databases in like ACD or
NCI or any other database you have available with 3D coordinates for 
suitable scaffold candidates for your CoMFA model.

Best regards,

Bernd

bwendt[at]tripos.com

Sent to CCL by: "Deepangi Pandit" [deepangi.pandit]*[gmail.com] Hi DD, I am not sure if you have tried this or looking for similar stuff but if you are using SYBYL there is an option for QSAR Optimization via option optimize QSAR. I do not remember the exact menu location but please search Tripos Bookshelf for QSAR optimization or optimize QSAR.
I think there is also a tutorial about the same.

Deepa



On Mon, Aug 18, 2008 at 10:30 AM, D dean ddean86 _ gmail.com <owner-chemistry#%#ccl.net> wrote:
>
> Sent to CCL by: "D  dean" [ddean86*|*gmail.com] Hello,
>
> I had performed a 3D-QSAR analysis and got favorable electropositive (blue) and electronegative (red) contour maps.
>
> I am interested to know if there are a list of scaffolds which I can use for substituting near favorable electropositive and favorable electronegative contour regions.
>
> Most of the 3D-QSAR paper just say favorable regions, or just suggest carbonyl group near electronegative and free amino group near electropositive regions.
>
> If anyone can suggest a listing of such scaffolds which I can try it will be very heplpful to me and maybe also helpful to other beginners.
>
> Thank you for your time.
>
> Best regards,
>
> DD>
>
>