From owner-chemistry@ccl.net Wed Feb  2 07:18:00 2011
From: "Val Gillet v.gillet{:}sheffield.ac.uk" <owner-chemistry _ server.ccl.net>
To: CCL
Subject: CCL: Chemoinformatics Short Course: Sheffield June 2011
Message-Id: <-43829-110202071556-10735-xOhILuT4mDVbU8zQKD0/gA _ server.ccl.net>
X-Original-From: "Val  Gillet" <v.gillet-,-sheffield.ac.uk>
Date: Wed, 2 Feb 2011 07:15:55 -0500


Sent to CCL by: "Val  Gillet" [v.gillet::sheffield.ac.uk]
      A Practical Introduction to Chemoinformatics
                  June 21st-24th, 2011
                The University of Sheffield
            http://cisrg.shef.ac.uk/chemcourse

The University of Sheffield will be hosting the above short course
which is supported by the Chemical Structure Association Trust (CSAT) and
the Molecular Graphics and Modelling Society (MGMS). This intensive short
course, which has been run since 2000, provides an introduction to the
major aspects of Chemoinformatics, with particular emphasis on applications
in modern drug discovery. The course will comprise a mixture of hands-on
workshops using state-of-the-art software, lectures, and informal
discussions and will be delivered by world leaders in the field from
academia and industry.

Please note that places on the course are limited and in previous years the
course has filled up very quickly so please register your interest as soon
as possible.

Two student bursaries will be available thanks to generous support provided
by the CSAT and the MGMS. Details on how to apply for these are available
on the website.

For further details see: http://cisrg.shef.ac.uk/chemcourse or contact
Val Gillet (v.gillet^sheffield.ac.uk)


From owner-chemistry@ccl.net Wed Feb  2 07:56:01 2011
From: "John john|-|ccdc.cam.ac.uk" <owner-chemistry .. server.ccl.net>
To: CCL
Subject: CCL: FW: How to get 3D structures of FDA approved drugs
Message-Id: <-43830-110202052657-8337-c1PLnQheUq39p9dpi+QvIQ .. server.ccl.net>
X-Original-From: "John" <john-x-ccdc.cam.ac.uk>
Content-Language: en-gb
Content-Transfer-Encoding: 7bit
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	charset="US-ASCII"
Date: Wed, 2 Feb 2011 10:26:38 -0000
MIME-Version: 1.0


Sent to CCL by: "John" [john**ccdc.cam.ac.uk]
Dear Anup,

         If you have a literature reference to the crystal structure
determination of a drug molecule you are interested in, you can download the
structure as deposited by the authors, from
http://www.ccdc.cam.ac.uk/products/csd/request/. You will need the CCDC
Deposition number which can be found in the literature reference.

         Some 3D structures of well known drugs are also accessible from the
CCDC Teaching Dataset. These can be best accessed by searching for the drug
of interest using Chemspider (http://www.chemspider.com) and then, via the
Xtal Structures tab of the entry of interest, accessing and downloading the
relevant structure.
         
          If you are able to access the Cambridge Structural Database (CSD)
> from your institution we could provide you with a list of CSD refcodes to 3D
structures of FDA approved compounds that we've compiled. Anyone interested
in accessing this list should contact CCDC at support : ccdc.cam.ac.uk.

  Should you need further information on how to access the CSD, please visit
http://www.ccdc.cam.ac.uk or e-mail admin : ccdc.cam.ac.uk

           John




-----Original Message-----
> From: owner-chemistry+ccdc-announce==ccdc.cam.ac.uk : ccl.net
[mailto:owner-chemistry+ccdc-announce==ccdc.cam.ac.uk : ccl.net] On Behalf Of
Anup Shah shahanup86#gmail.com
Sent: 27 January 2011 04:47
To: Rutland, Anne 
Subject: CCL: How to get 3D structures of FDA approved drugs


Sent to CCL by: "Anup  Shah" [shahanup86%x%gmail.com]
Hello all,

Can anybody suggest any source from which we can download 3D structures or 
crystal structures of FDA approved drugs?

Thanking you in anticipation



Regards

Anup Shah
IGIB, New Delhi,
Indiahttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtLEGAL NOTICE
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please inform postmaster : ccdc.cam.ac.uk and delete the message.
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by Guarantee and a Registered Charity.
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Registered office 12 Union Road, Cambridge CB2 1EZ.


From owner-chemistry@ccl.net Wed Feb  2 08:11:40 2011
From: "Eduard Matito ematito..gmail.com" <owner-chemistry|,|server.ccl.net>
To: CCL
Subject: CCL:G: number of digits in Gaussian output
Message-Id: <-43831-110201183015-13437-ywyS3C5lFBFDbtqcN2PB8w|,|server.ccl.net>
X-Original-From: Eduard Matito <ematito ~ gmail.com>
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Date: Wed, 2 Feb 2011 00:29:53 +0100
Mime-Version: 1.0 (Apple Message framework v936)


Sent to CCL by: Eduard Matito [ematito_._gmail.com]
Try to write the checkpoint file (Fchk). Some the quantities that are  
written there have more
precision than in the standard outputs. Of course it will only help if  
the quantities you want
are included in the fchk too. I guess normal modes are included in the  
fchk.

Otherwise I'm afraid you have to change the code and recompile.

Eduard

On Feb 1, 2011, at 10:38 PM, Leonid Shirkov leonid.shirkov!A! 
tiger.chem.uw.edu.pl wrote:

>
> Sent to CCL by: "Leonid  Shirkov" [leonid.shirkov _  
> tiger.chem.uw.edu.pl]
>
> Dear Colleagues,
>
> I need to have more digits after the decimal point in the Gaussian  
> output.
> For example, when I do PES Scan and have the final table, there are  
> only five digits. Of course, I can
> find more precise values in the output file, but I thought maybe  
> there is a way to define the precision
> in the final table.
> Another example is the eigenvectors in frequency analysis, by  
> default they are printed with 2 digits.
> Thank you in advance!
>
> Regards,
> Leonid
>
>
>
> -= This is automatically added to each message by the mailing script  
> =-
> To recover the email address of the author of the message, please  
> change> Conferences: http://server.ccl.net/chemistry/announcements/ 
> conferences/>
>

--
Eduard Matito
Postdoctoral researcher
Institute of Physics
University of Szczecin
Wielkopolska 15
70451 Szczecin (Poland)
Phone: +48914441436
http://ematito.webs.com


From owner-chemistry@ccl.net Wed Feb  2 08:30:00 2011
From: "Alex Naden anaden],[fsmail.net" <owner-chemistry/a\server.ccl.net>
To: CCL
Subject: CCL: Large .XYZ file visualization
Message-Id: <-43832-110202075959-16292-ZTztjF0l9bAggqqyWpRaCQ/a\server.ccl.net>
X-Original-From: "Alex  Naden" <anaden[#]fsmail.net>
Date: Wed, 2 Feb 2011 07:59:58 -0500


Sent to CCL by: "Alex  Naden" [anaden,+,fsmail.net]
Hello,

Could anyone recommend a software (Linux/ Windows) or on-line that is capable of handling very large .xyz files? 

Thank you,

Alex


From owner-chemistry@ccl.net Wed Feb  2 09:05:00 2011
From: "Jan Labanowski janl|*|speakeasy.net" <owner-chemistry . server.ccl.net>
To: CCL
Subject: CCL: CCL service interruption
Message-Id: <-43833-110202080325-19923-B1RHRwRIany0WkSsL81BfA . server.ccl.net>
X-Original-From: Jan Labanowski <janl]![speakeasy.net>
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Date: Wed, 02 Feb 2011 08:03:19 EST
MIME-Version: 1.0


Sent to CCL by: Jan Labanowski [janl#speakeasy.net]
Dear CCL,
We have winter ice storm in Ohio and power lines are going 
down under heavy weight of ice. Driving is difficult and 
schools are closed. While people in the Western hemisphere 
may not have noticed, the CCL was down for several hours 
this night, since I did not have power. Now the power is 
back. Please keep your fingers crossed that it stays this 
way, or I will have to get my portable generator from the 
garage...

Jan
--
Jan Labanowski
CCL Manager
jkl(~)ccl.net


From owner-chemistry@ccl.net Wed Feb  2 09:40:01 2011
From: "Jose Goncalo Deira Duarte de Campos Justino jgcj|fct.unl.pt" <owner-chemistry_+_server.ccl.net>
To: CCL
Subject: CCL: MOPAC and metals
Message-Id: <-43834-110202073420-23705-fSLQTAUCYIujRnwqltiDHQ_+_server.ccl.net>
X-Original-From: "Jose Goncalo Deira Duarte de Campos Justino" <jgcj!^!fct.unl.pt>
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Date: Wed, 2 Feb 2011 12:34:10 -0000 (WET)
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Sent to CCL by: "Jose Goncalo Deira Duarte de Campos Justino" [jgcj:_:fct.unl.pt]
Dear all,

I've been thinking about using mopac2009 to model some iron-porphyrin
systems. The aim so far is to check how the software behaves. I'm quite
familiar with mopac by now, but the metal atom has been triggering some
questions.

Formally, I have an iron (IV) atom complexed equatorially by the 4 N atoms
> from porphyrin (which has a radical cation delocalized over the aromatic
part and two anionic carboxylate groups) and, apically, by a HS-
(thiolate) group and an O atom (formal charge -2). This should be neutral.
(for those of you who might recognize, it's derived from the P450 compound
I active site).

Playing with mopac and mozyme and related keywords from the manual, I
never get a Fe(IV) state but a Fe(II) state. Is there anyway to set  this
in the input file?

My best try so far got me a total charge of -3 with very good geometries,
so i threw in 3 K+ atoms, and the geometry remained excellent. What do you
feel about the validity of this approach ?

Paralell, is there any particular way to specify dative bonds in mopac
such as those of Fe to the porphyrin N atoms ? Is SETPI the best option
for these, or totally non-sense ?

Any input (any at all, really) is welcome!

All the best,
Gonçalo


From owner-chemistry@ccl.net Wed Feb  2 10:16:00 2011
From: "P.D.Jarowski-x-surrey.ac.uk" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL: VB2000 for ICT
Message-Id: <-43835-110202090551-18768-S7SFPOIkbJSa/zVUc7rYZw() server.ccl.net>
X-Original-From: <P.D.Jarowski,,surrey.ac.uk>
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Date: Wed, 2 Feb 2011 14:05:39 +0000
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Sent to CCL by: [P.D.Jarowski##surrey.ac.uk]
--_000_C96F1533E52pj0013surreyacuk_
Content-Type: text/plain; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

Dear All.

I am new to valence-bond theory. I have started to implement VB2000 to look=
 into some valence-bond structures of a common intramolecular charge transf=
er organic molecule. I am having great difficulty understanding how to cons=
truct the valence structures using multi-structure VB as implemented in VB2=
000.  I am trying to represent the ground state and the most important ict =
structure where a negative charge resides on a dicyanomethilidine and the p=
ositive charge on the dimethylammonium.  (you may need to load the structur=
e to understand) Am I even close? What other keywords will I need? Do I nee=
d to use Group Function Theory here? Any help would be much appreciated.

Thanks a lot,

Peter

Here is my input file:

#! VB(16)/sto-3g PRINTALL

Multi-structure VB on parent ICT

0 1
 6     3.563680     1.141199    -0.572289
 6     2.621660     1.846249     0.219742
 6     1.353289     1.336271     0.431174
 6     0.933208     0.106721    -0.120267
 6     1.876447    -0.591072    -0.908703
 6     3.146954    -0.098015    -1.130923
 6    -0.403269    -0.369136     0.138772
 6    -0.984818    -1.523489    -0.303534
 6    -2.323381    -1.863636     0.035966
 6    -2.991754    -2.999993    -0.360778
 6    -4.341113    -3.234581     0.044904
 7    -5.441353    -3.415245     0.381893
 7     4.827129     1.632924    -0.792194
 6     5.772546     0.887686    -1.610742
 6    -2.368274    -3.984922    -1.188824
 7    -1.835295    -4.770468    -1.863661
 6     5.229343     2.903781    -0.208745
 1     0.656231     1.903617     1.043960
 1     1.607515    -1.542408    -1.358036
 1     2.885525     2.795444     0.669595
 1     3.828262    -0.675645    -1.743500
 1    -2.876313    -1.169192     0.665391
 1     4.598596     3.730733    -0.562224
 1     5.179834     2.880541     0.888333
 1     6.259438     3.119340    -0.495099
 1     5.985874    -0.102260    -1.185661
 1     5.401103     0.747629    -2.634749
 1     6.711133     1.440397    -1.665373
 1    -1.011991     0.283540     0.766208
 1    -0.434020    -2.218369    -0.932359

$02PIVBO
16
1,2,3,4,5,6,7,8,9,10,11,12,13,15,16

$02VBSTR
4
1 2 3 4 5 6 7 8 9 10 11 12 13 13 14 15
1 13 13 13 2 3 4 7 5 6 8 9 10 10 11 12 14 15

--_000_C96F1533E52pj0013surreyacuk_
Content-Type: text/html; charset="iso-8859-1"
Content-Transfer-Encoding: quoted-printable

<HTML>
<HEAD>
<TITLE>VB2000 for ICT</TITLE>
</HEAD>
<BODY>
<FONT FACE=3D"Calibri, Verdana, Helvetica, Arial"><SPAN STYLE=3D'font-size:=
11pt'>Dear All.<BR>
<BR>
I am new to valence-bond theory. I have started to implement VB2000 to look=
 into some valence-bond structures of a common intramolecular charge transf=
er organic molecule. I am having great difficulty understanding how to cons=
truct the valence structures using multi-structure VB as implemented in VB2=
000. &nbsp;I am trying to represent the ground state and the most important=
 ict structure where a negative charge resides on a dicyanomethilidine and =
the positive charge on the dimethylammonium. &nbsp;(you may need to load th=
e structure to understand) Am I even close? What other keywords will I need=
? Do I need to use Group Function Theory here? Any help would be much appre=
ciated.<BR>
<BR>
Thanks a lot,<BR>
<BR>
Peter<BR>
<BR>
Here is my input file:<BR>
<BR>
</SPAN></FONT><FONT SIZE=3D"2"><FONT FACE=3D"Courier, Courier New"><SPAN ST=
YLE=3D'font-size:10pt'> #! VB(16)/sto-3g PRINTALL<BR>
<BR>
Multi-structure VB on parent ICT<BR>
<BR>
0 1<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;3.563680 &nbsp;&nbsp;&nbsp;&nbsp;1.141199 &=
nbsp;&nbsp;&nbsp;-0.572289<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;2.621660 &nbsp;&nbsp;&nbsp;&nbsp;1.846249 &=
nbsp;&nbsp;&nbsp;&nbsp;0.219742<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;1.353289 &nbsp;&nbsp;&nbsp;&nbsp;1.336271 &=
nbsp;&nbsp;&nbsp;&nbsp;0.431174<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;0.933208 &nbsp;&nbsp;&nbsp;&nbsp;0.106721 &=
nbsp;&nbsp;&nbsp;-0.120267<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;1.876447 &nbsp;&nbsp;&nbsp;-0.591072 &nbsp;=
&nbsp;&nbsp;-0.908703<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;3.146954 &nbsp;&nbsp;&nbsp;-0.098015 &nbsp;=
&nbsp;&nbsp;-1.130923<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-0.403269 &nbsp;&nbsp;&nbsp;-0.369136 &nbsp;&nbsp=
;&nbsp;&nbsp;0.138772<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-0.984818 &nbsp;&nbsp;&nbsp;-1.523489 &nbsp;&nbsp=
;&nbsp;-0.303534<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-2.323381 &nbsp;&nbsp;&nbsp;-1.863636 &nbsp;&nbsp=
;&nbsp;&nbsp;0.035966<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-2.991754 &nbsp;&nbsp;&nbsp;-2.999993 &nbsp;&nbsp=
;&nbsp;-0.360778<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-4.341113 &nbsp;&nbsp;&nbsp;-3.234581 &nbsp;&nbsp=
;&nbsp;&nbsp;0.044904<BR>
&nbsp;7 &nbsp;&nbsp;&nbsp;-5.441353 &nbsp;&nbsp;&nbsp;-3.415245 &nbsp;&nbsp=
;&nbsp;&nbsp;0.381893<BR>
&nbsp;7 &nbsp;&nbsp;&nbsp;&nbsp;4.827129 &nbsp;&nbsp;&nbsp;&nbsp;1.632924 &=
nbsp;&nbsp;&nbsp;-0.792194<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;5.772546 &nbsp;&nbsp;&nbsp;&nbsp;0.887686 &=
nbsp;&nbsp;&nbsp;-1.610742<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;-2.368274 &nbsp;&nbsp;&nbsp;-3.984922 &nbsp;&nbsp=
;&nbsp;-1.188824<BR>
&nbsp;7 &nbsp;&nbsp;&nbsp;-1.835295 &nbsp;&nbsp;&nbsp;-4.770468 &nbsp;&nbsp=
;&nbsp;-1.863661<BR>
&nbsp;6 &nbsp;&nbsp;&nbsp;&nbsp;5.229343 &nbsp;&nbsp;&nbsp;&nbsp;2.903781 &=
nbsp;&nbsp;&nbsp;-0.208745<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;0.656231 &nbsp;&nbsp;&nbsp;&nbsp;1.903617 &=
nbsp;&nbsp;&nbsp;&nbsp;1.043960<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;1.607515 &nbsp;&nbsp;&nbsp;-1.542408 &nbsp;=
&nbsp;&nbsp;-1.358036<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;2.885525 &nbsp;&nbsp;&nbsp;&nbsp;2.795444 &=
nbsp;&nbsp;&nbsp;&nbsp;0.669595<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;3.828262 &nbsp;&nbsp;&nbsp;-0.675645 &nbsp;=
&nbsp;&nbsp;-1.743500<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;-2.876313 &nbsp;&nbsp;&nbsp;-1.169192 &nbsp;&nbsp=
;&nbsp;&nbsp;0.665391<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;4.598596 &nbsp;&nbsp;&nbsp;&nbsp;3.730733 &=
nbsp;&nbsp;&nbsp;-0.562224<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;5.179834 &nbsp;&nbsp;&nbsp;&nbsp;2.880541 &=
nbsp;&nbsp;&nbsp;&nbsp;0.888333<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;6.259438 &nbsp;&nbsp;&nbsp;&nbsp;3.119340 &=
nbsp;&nbsp;&nbsp;-0.495099<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;5.985874 &nbsp;&nbsp;&nbsp;-0.102260 &nbsp;=
&nbsp;&nbsp;-1.185661<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;5.401103 &nbsp;&nbsp;&nbsp;&nbsp;0.747629 &=
nbsp;&nbsp;&nbsp;-2.634749<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;&nbsp;6.711133 &nbsp;&nbsp;&nbsp;&nbsp;1.440397 &=
nbsp;&nbsp;&nbsp;-1.665373<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;-1.011991 &nbsp;&nbsp;&nbsp;&nbsp;0.283540 &nbsp;=
&nbsp;&nbsp;&nbsp;0.766208<BR>
&nbsp;1 &nbsp;&nbsp;&nbsp;-0.434020 &nbsp;&nbsp;&nbsp;-2.218369 &nbsp;&nbsp=
;&nbsp;-0.932359<BR>
<BR>
$02PIVBO<BR>
16<BR>
1,2,3,4,5,6,7,8,9,10,11,12,13,15,16<BR>
<BR>
$02VBSTR<BR>
4<BR>
1 2 3 4 5 6 7 8 9 10 11 12 13 13 14 15<BR>
1 13 13 13 2 3 4 7 5 6 8 9 10 10 11 12 14 15</SPAN></FONT></FONT>
</BODY>
</HTML>


--_000_C96F1533E52pj0013surreyacuk_--


From owner-chemistry@ccl.net Wed Feb  2 10:51:01 2011
From: "Esteban Gabriel Vega Hissi egvega]^[gmail.com" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: Large .XYZ file visualization
Message-Id: <-43836-110202094541-5538-wfj7sD7Fi0lDGmsq44M44g- -server.ccl.net>
X-Original-From: Esteban Gabriel Vega Hissi <egvega{:}gmail.com>
Content-Type: multipart/alternative; boundary=20cf30433f1a881546049b4db322
Date: Wed, 2 Feb 2011 11:45:13 -0300
MIME-Version: 1.0


Sent to CCL by: Esteban Gabriel Vega Hissi [egvega]![gmail.com]
--20cf30433f1a881546049b4db322
Content-Type: text/plain; charset=ISO-8859-1

Hi,

How large is your file?
Anyway, try: pymol or VMD

Hope this help

Biochemist Esteban G. Vega-Hissi
UNSL
Argentina

--

On Wed, Feb 2, 2011 at 9:59 AM, Alex Naden anaden],[fsmail.net <
owner-chemistry{}ccl.net> wrote:

>
> Sent to CCL by: "Alex  Naden" [anaden,+,fsmail.net]
> Hello,
>
> Could anyone recommend a software (Linux/ Windows) or on-line that is
> capable of handling very large .xyz files?
>
> Thank you,
>
> Alex>
>
>

--20cf30433f1a881546049b4db322
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Hi,<br><br>How large is your file?<br>Anyway, try: pymol or VMD<br><br>Hope=
 this help<br><br>Biochemist Esteban G. Vega-Hissi<br>UNSL<br>Argentina<br>=
<br>--<br><br><div class=3D"gmail_quote">On Wed, Feb 2, 2011 at 9:59 AM, Al=
ex Naden anaden],[<a href=3D"http://fsmail.net">fsmail.net</a> <span dir=3D=
"ltr">&lt;<a href=3D"mailto:owner-chemistry{}ccl.net">owner-chemistry{}ccl.ne=
t</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt 0.8ex; borde=
r-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><br>
Sent to CCL by: &quot;Alex =A0Naden&quot; [anaden,+,<a href=3D"http://fsmai=
l.net" target=3D"_blank">fsmail.net</a>]<br>
Hello,<br>
<br>
Could anyone recommend a software (Linux/ Windows) or on-line that is capab=
le of handling very large .xyz files?<br>
<br>
Thank you,<br>
<br>
Alex<br>
<br>
<br>
<br>
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--20cf30433f1a881546049b4db322--


From owner-chemistry@ccl.net Wed Feb  2 11:25:00 2011
From: "eurisco1:_:pochta.ru" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: Large .XYZ file visualization
Message-Id: <-43837-110202095114-11356-TCbATQXp7LPsZYB7ZF7MUg(0)server.ccl.net>
X-Original-From: <eurisco1_._pochta.ru>
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Date: Wed, 2 Feb 2011 17:50:58 +0300
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Sent to CCL by: [eurisco1~!~pochta.ru]
Dear Alex  Naden,

Maybe Rasmol is suitable.

Sincerely,
Ol Ga


-----éÓÈÏÄÎÏÅ ÓÏÏÂÝÅÎÉÅ----- 
> From: Alex Naden anaden],[fsmail.net
Sent: Wednesday, February 02, 2011 3:59 PM
To: Ga, Ol 
Subject: CCL: Large .XYZ file visualization


Sent to CCL by: "Alex  Naden" [anaden,+,fsmail.net]
Hello,

Could anyone recommend a software (Linux/ Windows) or on-line that is 
capable of handling very large .xyz files?

Thank you,

Alexhttp://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 Wed Feb  2 12:34:01 2011
From: "Close, David M. CLOSED~~mail.etsu.edu" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: dissenting results
Message-Id: <-43838-110202123234-21771-bjC6uj7NpIFy8q5EzADyIw],[server.ccl.net>
X-Original-From: "Close, David M." <CLOSED|*|mail.etsu.edu>
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Date: Wed, 2 Feb 2011 17:32:13 +0000
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Sent to CCL by: "Close, David M." [CLOSED!A!mail.etsu.edu]
This is very interesting.  But you need to tell us how much the numbers differ.  I can see how sometimes very small difference could arise from coding errors arising from one subroutine using a double precision variable, and another subroutine using the same variable with a different word-length.  But these would be very small differences.  Give us an example of how big the differences are, and what keywords are used to control the accuracy of each SCF cycle.
  Regards, Dave Close.

-----Original Message-----
> From: owner-chemistry+closed==etsu.edu]-[ccl.net [mailto:owner-chemistry+closed==etsu.edu]-[ccl.net] On Behalf Of Lukman Olawale Olasunkanm waleolasunkanmi:gmail.com
Sent: Tuesday, February 01, 2011 8:43 AM
To: Close, David M.
Subject: CCL: dissenting results


Sent to CCL by: "Lukman Olawale Olasunkanm" [waleolasunkanmi#,#gmail.com]
Hello everyone,
I usually run my MOPAC job twice: first for ordinary optimization from which I normally get the GNORM value ( and H.O.F., dipole moments, HOMO-LUMO, COSMOS Area and volume etc.), and second for the thermo values (with the specified value of the GNORM using the LET keyword). I discovered that the values got for the common parameters like H.O.F, dipole moments etc. in both cases differ.
What can you advise me to do please?
Thank youhttp://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 Wed Feb  2 14:40:00 2011
From: "Ken Butenhof Ken.Butenhof[-]accelrys.com" <owner-chemistry---server.ccl.net>
To: CCL
Subject: CCL: Large .XYZ file visualization
Message-Id: <-43839-110202122412-10316-gnj+5L9ixXE0dGg0NMHGlQ---server.ccl.net>
X-Original-From: Ken Butenhof <Ken.Butenhof .. accelrys.com>
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Date: Wed, 2 Feb 2011 09:23:46 -0800
MIME-Version: 1.0


Sent to CCL by: Ken Butenhof [Ken.Butenhof*accelrys.com]
Alex,

I'm not sure what you mean by "very large" -- perhaps either a large molecule or a long trajectory, or both.

Discovery Studio 3.0 is a free visualization client available from Accelrys that runs on both Windows and Linux environments and works well for large molecules and long trajectories.  For example I have worked with trajectories of full length antibodies.  DS does support .xyz format, though I do not have any experience using the .xyz format for large molecules or trajectories.   The xyz format itself does not contain residue based information, and is limited in other ways as well. For large molecules a different format such as pdb or mol2 might be better.   DS supports a wide range of file formats.  You can download it here:

http://accelrys.com/products/discovery-studio/visualization-download.php


Best wishes,

Ken

Kenneth Butenhof, Ph. D.
Principal Scientist,
Accelrys, Inc.

office 603 647-8882
cell   603 965-6600

-----Original Message-----
> From: owner-chemistry+kenb==accelrys.com]|[ccl.net [mailto:owner-chemistry+kenb==accelrys.com]|[ccl.net] On Behalf Of Alex Naden anaden],[fsmail.net
Sent: Wednesday, February 02, 2011 8:00 AM
To: Ken Butenhof
Subject: CCL: Large .XYZ file visualization


Sent to CCL by: "Alex  Naden" [anaden,+,fsmail.net]
Hello,

Could anyone recommend a software (Linux/ Windows) or on-line that is capable of handling very large .xyz files? 

Thank you,

Alexhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt