From owner-chemistry@ccl.net Wed Jul  1 04:05:01 2009
From: "selva raj selvacbm%a%yahoo.co.in" <owner-chemistry- -server.ccl.net>
To: CCL
Subject: CCL: dear sir
Message-Id: <-39665-090701040345-8961-cj9X1MRkMVAZGFxIFBODbw- -server.ccl.net>
X-Original-From: "selva  raj" <selvacbm() yahoo.co.in>
Date: Wed, 1 Jul 2009 04:03:42 -0400


Sent to CCL by: "selva  raj" [selvacbm],[yahoo.co.in]
Dear Sir
        I have some doubt,How do calculate these type of accessible surface 
area
Accessible surface areas (ASA) for the uncomplexed and complexed forms
of the protein in A2
Residue  Uncomplexed   Complexed  % change
Glu 35    42.24        32.63        22.8
Asp52     17.47         9.53        45.4
Gln 57    15.32         1.42        90.7
 Ile 58    4.41         0.66        85.0
Asn59     31.76        15.84        50.1
Trp62    112.7        108.77         3.50
Trp63     33.96        21.21        37.5
Ile98     11.96        6.68         44.2
Ala107    52.94       20.82         60.7
Trp108    12.61        1.01         92.0
Val109    82.20       68.19         17.0
Residues losing more than 60% ASA on complex formation are in bold

The accessible surface area (ASA) of the protein and the docked complex were 
calculated using NACCESS . The differences in  ASA of residues that are 
involved in ligand binding are
calculated as ASAi = ASAi uncomplexed - ASAi complexed.

These type of ASA calculation we have to  done our project, If you know means 
please tell me the answer.


From owner-chemistry@ccl.net Wed Jul  1 04:42:01 2009
From: "Aditya Khandavelli svk003*|*latech.edu" <owner-chemistry-$-server.ccl.net>
To: CCL
Subject: CCL: error in TD-DFT calculations- Please help
Message-Id: <-39666-090701032652-4600-WzIHBWosNj3dJKlk+ONdFA-$-server.ccl.net>
X-Original-From: "Aditya  Khandavelli" <svk003:_:latech.edu>
Date: Wed, 1 Jul 2009 03:26:48 -0400


Sent to CCL by: "Aditya  Khandavelli" [svk003|-|latech.edu]
Dear All,

I was running TD-DFT calculations. I was able to get the first three excited 
states. When I was trying to Optimize the first excited state, the 
calculation ended up with an error which is as follows

 HESSIAN DOES NOT HAVE THE DESIRED LOCAL STRUCTURE
 TAKING SIMPLE RFO STEP
 SEARCHING FOR LAMDA THAT MINIMIZES ALONG ALL MODES


 *****************************************
 *** UNABLE TO DETERMINE LAMDA IN FmD114 **
 *****************************************

My second part of the input is as follows,

--Link1--
%Chk=firstex.chk
%NoSave
#p TD=(Root=1, Read) B3LYP Opt=Maxcycle=1024 Freq Scfcyc=1024 Geom=Check 
Guess=Read Test

In the first part of my simulation, i've calculated the excited states of the 
system.

Please help me out in this regard. Kindly acknowledge.

regards,
Aditya Khandavelli.


From owner-chemistry@ccl.net Wed Jul  1 05:23:01 2009
From: "=?ISO-8859-1?Q?Philippe_Carbonni=E8re?= philippe.carbonniere[-]univ-pau.fr" <owner-chemistry ~~ server.ccl.net>
To: CCL
Subject: CCL: symposium : computational aspects of the modelling of vibrational properties.
Message-Id: <-39667-090701044234-27887-yr8bpWrS2E1IMva4vjgFuw ~~ server.ccl.net>
X-Original-From: =?ISO-8859-1?Q?Philippe_Carbonni=E8re?=
 <philippe.carbonniere-*-univ-pau.fr>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Date: Wed, 01 Jul 2009 10:41:48 +0200
MIME-Version: 1.0


Sent to CCL by: =?ISO-8859-1?Q?Philippe_Carbonni=E8re?=
 [philippe.carbonniere-#-univ-pau.fr]
Please note the following international symposium :

"Computational aspects of the modelling of vibrational properties of
gases, liquids and solids"

which will be held in "Seventh International Conference of Computational
Methods in Sciences and Engineering" (http://www.iccmse.org/)

at Hotel Rodos Palace, Rodos, Greece. from September 29 to October 4, 2009.

Invited speakers :

Pr. Bowman, J.M.
Pr. Carrington, T.
Pr. Champagne, B.
Pr. Christiansen, O.
Dr. Dal Corso, A.
Pr. Dolgusheva, E.
Pr. Dovesi, R.
Dr. Gaspari, F.
Dr. Gatti, F.
Pr. Gonze, X.
Pr. Hochlaf, M.
Dr. Jalkanen, K. J.
Pr. Janezic, D.
Dr. Lauvergnat, D.
Dr. Matito, E.
Pr. Pasquarello, A.
Dr. Puzzarini, C.
Pr. Schofield, D.
Dr. Shiga, M.
Pr. tavan, P.
Pr. Torii, H.
Dr. Ghysels, A.
Pr. Yagi, K.

Submission of a short abstract is welcome for interested persons.

Organizers : Philippe Carbonniere and Claude Pouchan, IPREM, Pau
University, France
and
Mauro Causa, University "Federico II", Naples, Italy

Contact
philippe.carbonniere{=}univ-pau.fr


From owner-chemistry@ccl.net Wed Jul  1 08:05:01 2009
From: "Hai-Bin Li lihb734^yahoo.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate the emission spectra?
Message-Id: <-39668-090701065128-25916-nrUZlgP0Ja1ajWeUVJqFVA]|[server.ccl.net>
X-Original-From: "Hai-Bin  Li" <lihb734-x-yahoo.com>
Date: Wed, 1 Jul 2009 06:51:25 -0400


Sent to CCL by: "Hai-Bin  Li" [lihb734-x-yahoo.com]
Dear All Subscriber:
 I am newbie to computational chemistry. What I should do to calculate the emission spectra by use of Gaussian03 or ADF2008.01? Is there any free auxil programme to investigate the vibronic-structure spectrum? Thank you in advance.


From owner-chemistry@ccl.net Wed Jul  1 08:40:01 2009
From: "Lee Ji Young jiyoung84^^^yonsei.ac.kr" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Questions about AutoDock
Message-Id: <-39669-090701040921-10912-ffvouW64MN7TXm0qGrrflA]|[server.ccl.net>
X-Original-From: "Lee  Ji Young" <jiyoung84||yonsei.ac.kr>
Date: Wed, 1 Jul 2009 04:09:14 -0400


Sent to CCL by: "Lee  Ji Young" [jiyoung84\a/yonsei.ac.kr]
Hello

I have a question about using autodock 4.2

Now i am working to find inhibitors against Avian influenza virus.

So i want to use autodock 4.2

My protein-receptor- has one magnesium ion in the binding pocket, but i have no idea how to manage it.

To dock a inhibitor the receptor with the magnesium ion, what can i do?

How can i assing metal ion, and its charge?

please give me a piece of advice.

Thank you

My name : Ji Young Lee
email : jiyoung84##yonsei.ac.kr
address : Engineering building B408, Yonsei university, Shinchondong, Sudaemungu, Seoul, Korea


From owner-chemistry@ccl.net Wed Jul  1 09:16:01 2009
From: "Lee Ji Young jiyoung84]-[yonsei.ac.kr" <owner-chemistry(a)server.ccl.net>
To: CCL
Subject: CCL: Questions about AutoDock
Message-Id: <-39670-090701040922-10965-IzrrMKdTDfXTv5SN35uc8A(a)server.ccl.net>
X-Original-From: "Lee  Ji Young" <jiyoung84/./yonsei.ac.kr>
Date: Wed, 1 Jul 2009 04:09:19 -0400


Sent to CCL by: "Lee  Ji Young" [jiyoung84%x%yonsei.ac.kr]
Hello

I have a question about using autodock 4.2

Now i am working to find inhibitors against Avian influenza virus.

So i want to use autodock 4.2

My protein-receptor- has one magnesium ion in the binding pocket, but i have no idea how to manage it.

To dock a inhibitor the receptor with the magnesium ion, what can i do?

How can i assing metal ion, and its charge?

please give me a piece of advice.

Thank you

My name : Ji Young Lee
email : jiyoung84\a/yonsei.ac.kr
address : Engineering building B408, Yonsei university, Shinchondong, Sudaemungu, Seoul, Korea


From owner-chemistry@ccl.net Wed Jul  1 10:21:00 2009
From: "laura S slaurami+*+yahoo.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL: Questions about AutoDock
Message-Id: <-39671-090701101742-20294-8MzqK1nfpJreiHH4iB4Pzw[A]server.ccl.net>
X-Original-From: laura S <slaurami%yahoo.com>
Content-Type: multipart/alternative; boundary="0-83169285-1246457846=:61680"
Date: Wed, 1 Jul 2009 07:17:26 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: laura S [slaurami() yahoo.com]

--0-83169285-1246457846=:61680
Content-Type: text/plain; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Ji Young Lee,=0A=0AI think you should edit the pdbqt file, were you ca=
n insert the good charge of the magnesium ion. I used this method in the ca=
se of AutoDock 4.0 (in my case was about a Zn2+ ion), but the software work=
s better without any water molecule or any ion.=0A=0AHope this helps,=0A=0A=
Amalia=0A=0A =0AAmalia-Laura Seff =0A--------------------------------------=
----------=0APhD student=0ABabes-Bolyai University=0A=0AFaculty of Chemistr=
y and Chemical Engineering =0AInorganic Chemistry Department=0AMolecular Mo=
deling Laboratory 101=0A =0AAdress: Arany J=E1nos Str. no. 11=0A           =
 Ro - 400028, Cluj-Napoca=0Atel: 40-264-593833/5772=0A      40-724752988=0A=
      36-702260428=0Afax: 40-264-590818=0A =0A=0A=0A=0A=0A_________________=
_______________=0AFrom: Lee Ji Young jiyoung84^^^yonsei.ac.kr <owner-chemis=
try]~[ccl.net>=0ATo: "Seff, Amalia Laura " <slaurami]~[yahoo.com>=0ASen=
t: Wednesday, July 1, 2009 11:09:14 AM=0ASubject: CCL: Questions about Auto=
Dock=0A=0A=0ASent to CCL by: "Lee  Ji Young" [jiyoung84\a/yonsei.ac.kr]=0AH=
ello=0A=0AI have a question about using autodock 4.2=0A=0ANow i am working =
to find inhibitors against Avian influenza virus.=0A=0ASo i want to use aut=
odock 4.2=0A=0AMy protein-receptor- has one magnesium ion in the binding po=
cket, but i have no idea how to manage it.=0A=0ATo dock a inhibitor the rec=
eptor with the magnesium ion, what can i do?=0A=0AHow can i assing metal io=
n, and its charge?=0A=0Aplease give me a piece of advice.=0A=0AThank you=0A=
=0AMy name : Ji Young Lee=0Aemail : jiyoung84^yonsei.ac.kr=0Aaddress : Engi=
neering building B408, Yonsei university, Shinchondong, Sudaemungu, Seoul, =
Korea=0A=0A=0A=0A-=3D This is automatically added to each message by the ma=
iling script =3D-=0ATo recover the email address of the author of the messa=
ge, please change=0Athe strange characters on the top line to the ]~[ sign. Y=
ou can also=0A=0A=0AE-=
mail to subscribers: CHEMISTRY]~[ccl.net or use:=0A      http://www.ccl.net/c=
gi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: CHEMISTRY-REQUES=
T]~[ccl.net or use=0A=0A=
=0A=0A      http://www.ccl.net/chemistry/sub_unsub.s=
html=0A=0A=0A=0AJob: =
http://www.ccl.net/jobs =0AConferences: http://server.ccl.net/chemistry/ann=
ouncements/conferences/=0A=0ASearch Messages: http://www.ccl.net/chemistry/=
searchccl/index.shtml=0A=0AIf your mail bounces from CCL with 5.7.1 error, =
check:=0A=0A=0ARTFI: http://www.ccl.ne=
t/chemistry/aboutccl/instructions/=0A=0A=0A      
--0-83169285-1246457846=:61680
Content-Type: text/html; charset=iso-8859-1
Content-Transfer-Encoding: quoted-printable

<html><head><style type=3D"text/css"><!-- DIV {margin:0px;} --></style></he=
ad><body><div style=3D"font-family:times new roman,new york,times,serif;fon=
t-size:10pt">Dear Ji Young Lee,<br><br>I think you should edit the pdbqt fi=
le, were you can insert the good charge of the magnesium ion. I used this m=
ethod in the case of AutoDock 4.0 (in my case was about a Zn2+ ion), but th=
e software works better without any water molecule or any ion.<br><br>Hope =
this helps,<br><br>Amalia<br><div>&nbsp;</div><div><strong>Amalia-Laura Sef=
f</strong> <em><br>------------------------------------------------<br></em=
><em><font color=3D"#823857"><span style=3D"color: rgb(91, 91, 91);">PhD st=
udent</span></font></em></div>  <div style=3D"color: rgb(91, 91, 91);">Babe=
s-Bolyai University<br></div>  <div style=3D"color: rgb(91, 91, 91);">Facul=
ty of Chemistry and Chemical Engineering </div>  <div style=3D"color: rgb(9=
1, 91, 91);">Inorganic Chemistry Department</div>  <div style=3D"color: rgb=
(91, 91,
 91);">Molecular Modeling Laboratory 101</div>  <div><font color=3D"#bf00bf=
"></font>&nbsp;</div>  <div><u>Adress</u>: Arany J=E1nos Str. no. 11</div> =
 <div>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Ro=
 - 400028, Cluj-Napoca</div>  <div><u>tel</u>: 40-264-593833/5772</div>  <d=
iv>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;40-724752988</div>  <div>&nbsp;&nbsp=
;&nbsp;&nbsp;&nbsp;&nbsp;36-702260428</div>  <div><u>fax</u>:&nbsp;40-264-5=
90818</div>  <div>&nbsp;</div><div><br></div><div style=3D"font-family: tim=
es new roman,new york,times,serif; font-size: 10pt;"><br><div style=3D"font=
-family: arial,helvetica,sans-serif; font-size: 10pt;"><font size=3D"2" fac=
e=3D"Tahoma"><hr size=3D"1"><b><span style=3D"font-weight: bold;">From:</sp=
an></b> Lee Ji Young jiyoung84^^^yonsei.ac.kr &lt;owner-chemistry]~[ccl.net&g=
t;<br><b><span style=3D"font-weight: bold;">To:</span></b> "Seff, Amalia La=
ura " &lt;slaurami]~[yahoo.com&gt;<br><b><span style=3D"font-weight:
 bold;">Sent:</span></b> Wednesday, July 1, 2009 11:09:14 AM<br><b><span st=
yle=3D"font-weight: bold;">Subject:</span></b> CCL: Questions about AutoDoc=
k<br></font><br>=0A<br>Sent to CCL by: "Lee&nbsp; Ji Young" [jiyoung84\a/yo=
nsei.ac.kr]<br>Hello<br><br>I have a question about using autodock 4.2<br><=
br>Now i am working to find inhibitors against Avian influenza virus.<br><b=
r>So i want to use autodock 4.2<br><br>My protein-receptor- has one magnesi=
um ion in the binding pocket, but i have no idea how to manage it.<br><br>T=
o dock a inhibitor the receptor with the magnesium ion, what can i do?<br><=
br>How can i assing metal ion, and its charge?<br><br>please give me a piec=
e of advice.<br><br>Thank you<br><br>My name : Ji Young Lee<br>email : jiyo=
ung84^yonsei.ac.kr<br>address : Engineering building B408, Yonsei universit=
y, Shinchondong, Sudaemungu, Seoul, Korea<br><br><br><br>-=3D This is autom=
atically added to each message by the mailing script =3D-<br>To recover the=
 email address of the author of the message, please change<br>the strange c=
haracters on the top line to the ]~[ sign. You can also<br>look up the X-Orig=
inal-From: line
 in the mail header.<br><br>E-mail to subscribers: <a ymailto=3D"mailto:CHE=
MISTRY]~[ccl.net" href=3D"mailto:CHEMISTRY]~[ccl.net">CHEMISTRY]~[ccl.net</a> or =
use:<br><span>&nbsp; &nbsp; &nbsp; <a target=3D"_blank" href=3D"http://www.=
ccl.net/cgi-bin/ccl/send_ccl_message">http://www.ccl.net/cgi-bin/ccl/send_c=
cl_message</a></span><br><br>E-mail to administrators: <a ymailto=3D"mailto=
:CHEMISTRY-REQUEST]~[ccl.net" href=3D"mailto:CHEMISTRY-REQUEST]~[ccl.net">CHEMI=
STRY-REQUEST]~[ccl.net</a> or use<br>&nbsp; &nbsp; &nbsp; <a href=3D"http://w=
ww.ccl.net/cgi-bin/ccl/send_ccl_message" target=3D"_blank">http://www.ccl.n=
et/cgi-bin/ccl/send_ccl_message</a><br><br<br><span=
>&nbsp; &nbsp; &nbsp; <a target=3D"_blank" href=3D"http://www.ccl.net/chemi=
stry/sub_unsub.shtml">http://www.ccl.net/chemistry/sub_unsub.shtml</a></spa=
n><br><br><span>Before posting, check wait time at: <a target=3D"_blank" hr=
ef=3D"http://www.ccl.net">http://www.ccl.net</a></span><br><br><span>Job: <=
a target=3D"_blank"
 href=3D"http://www.ccl.net/jobs">http://www.ccl.net/jobs</a> </span><br><s=
pan>Conferences: <a target=3D"_blank" href=3D"http://server.ccl.net/chemist=
ry/announcements/conferences/">http://server.ccl.net/chemistry/announcement=
s/conferences/</a></span><br><br><span>Search Messages: <a target=3D"_blank=
" href=3D"http://www.ccl.net/chemistry/searchccl/index.shtml">http://www.cc=
l.net/chemistry/searchccl/index.shtml</a></span><br><br>If your mail bounce=
s from CCL with 5.7.1 error, check:<br><span>&nbsp; &nbsp; &nbsp; <a target=
=3D"_blank" href=3D"http://www.ccl.net/spammers.txt">http://www.ccl.net/spa=
mmers.txt</a></span><br><br><span>RTFI: <a target=3D"_blank" href=3D"http:/=
/www.ccl.net/chemistry/aboutccl/instructions/">http://www.ccl.net/chemistry=
/aboutccl/instructions/</a></span><br><br><br></div></div></div><br>=0A=0A=
=0A=0A      </body></html>
--0-83169285-1246457846=:61680--


From owner-chemistry@ccl.net Wed Jul  1 11:41:01 2009
From: "David Gallagher gallagher.da-$-gmail.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate the emission spectra?
Message-Id: <-39672-090701113556-22182-/g4lbIUpJUNpwVImvZRD1Q..server.ccl.net>
X-Original-From: David Gallagher <gallagher.da .. gmail.com>
Content-Type: text/plain; charset="us-ascii"; format=flowed
Date: Wed, 01 Jul 2009 08:35:39 -0700
Mime-Version: 1.0


Sent to CCL by: David Gallagher [gallagher.da+/-gmail.com]
By emission spectra, if you mean fluorescence, then you would need to 
start by calculating the first excited state singlet geometry.  As 
the selection rules for absorption and fluorescence are the same, the 
absorption spectrum (calculated by ZINDO or INDO-S, for example) of 
the excited state geometry can be assumed to equate to the pure 
electronic fluorescence spectrum.  I am not aware of any free 
programs that can calculate vibronic spectra automatically, but 
perhaps someone else knows of one.  There are some slides 
illustrating how to calculate the electronic fluorescence spectra of 
fluorescein at http://www.cacheresearch.com/presentations.html 
.  Although, this example uses MOPAC and ZINDO, the principles would 
be similar for any quantum chemistry method.  Be aware that the 
accuracy of the predicted lambda-max can vary for a variety of 
reasons that are also covered in the slides.

I hope this helps,
David Gallagher
CACheResearch.com



At 03:51 AM 7/1/2009, Hai-Bin Li lihb734^yahoo.com wrote:

>Sent to CCL by: "Hai-Bin  Li" [lihb734-x-yahoo.com]
>Dear All Subscriber:
>  I am newbie to computational chemistry. What I should do to 
> calculate the emission spectra by use of Gaussian03 or ADF2008.01? 
> Is there any free auxil programme to investigate the 
> vibronic-structure spectrum? Thank you in advance.

From owner-chemistry@ccl.net Wed Jul  1 12:30:00 2009
From: "Frank Neese neese[A]thch.uni-bonn.de" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL:G: how to calculate the emission spectra?
Message-Id: <-39673-090701122854-14026-vHw37uiVNlpHiuGnaViDIA__server.ccl.net>
X-Original-From: Frank Neese <neese^_^thch.uni-bonn.de>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 01 Jul 2009 18:30:26 +0200
MIME-Version: 1.0


Sent to CCL by: Frank Neese [neese_-_thch.uni-bonn.de]
Dear Hai-Bin Li
>>  I am newbie to computational chemistry. What I should do to
>> calculate the emission spectra by use of Gaussian03 or ADF2008.01? Is
>> there any free auxil programme to investigate the vibronic-structure
>> spectrum? Thank you in advance.
ORCA is a free quantum chemistry program that can calculate vibronic
structure (download at http://www.thch.uni-bonn.de/tc/orca/). Be aware
that this is not a trivial calculation. The next release in the fall
will have a fully automatic and efficient procedure.

Best regards,
Frank Neese

-- 
-----------------------------------------------------------------
Prof. Dr. Frank Neese
Chair of Theoretical Chemistry
Department of Chemistry
University of Bonn
Wegelerstr. 12
D-53115 Bonn
Germany
E-Mail: neese _ thch.uni-bonn.de
URL: http://www.thch.uni-bonn.de/tc/
Telephone: +49-228-732351
-----------------------------------------------------------------


From owner-chemistry@ccl.net Wed Jul  1 13:18:01 2009
From: "Deepangi Pandit deepangi.pandit]-[gmail.com" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: dear sir
Message-Id: <-39674-090701121745-9541-w7cKBpxAa3daA/RbQ5k0ow(~)server.ccl.net>
X-Original-From: Deepangi Pandit <deepangi.pandit()gmail.com>
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 1 Jul 2009 11:45:22 -0400
MIME-Version: 1.0


Sent to CCL by: Deepangi Pandit [deepangi.pandit,,gmail.com]
Hi SelvaRaj:

Please refer the page below about NACCESS.

http://www.bioinf.manchester.ac.uk/naccess/

However, ASA can be calculated using other programs too. Some examples
below. Please refer the link for more information.



MGL TOOLS
http://mgltools.scripps.edu/

MOLMOL
http://www.msg.ucsf.edu/local/programs/molmol/manual.html

http://www.tucows.com/download.html?software_id=3D9805&file_id=3D&download=
=3Dautomatic

THX
DP









On Wed, Jul 1, 2009 at 4:03 AM, selva raj
selvacbm%a%yahoo.co.in<owner-chemistry]|[ccl.net> wrote:
>
> Sent to CCL by: "selva =A0raj" [selvacbm],[yahoo.co.in]
> Dear Sir
> =A0 =A0 =A0 =A0I have some doubt,How do calculate these type of accessibl=
e surface
> area
> Accessible surface areas (ASA) for the uncomplexed and complexed forms
> of the protein in A2
> Residue =A0Uncomplexed =A0 Complexed =A0% change
> Glu 35 =A0 =A042.24 =A0 =A0 =A0 =A032.63 =A0 =A0 =A0 =A022.8
> Asp52 =A0 =A0 17.47 =A0 =A0 =A0 =A0 9.53 =A0 =A0 =A0 =A045.4
> Gln 57 =A0 =A015.32 =A0 =A0 =A0 =A0 1.42 =A0 =A0 =A0 =A090.7
> =A0Ile 58 =A0 =A04.41 =A0 =A0 =A0 =A0 0.66 =A0 =A0 =A0 =A085.0
> Asn59 =A0 =A0 31.76 =A0 =A0 =A0 =A015.84 =A0 =A0 =A0 =A050.1
> Trp62 =A0 =A0112.7 =A0 =A0 =A0 =A0108.77 =A0 =A0 =A0 =A0 3.50
> Trp63 =A0 =A0 33.96 =A0 =A0 =A0 =A021.21 =A0 =A0 =A0 =A037.5
> Ile98 =A0 =A0 11.96 =A0 =A0 =A0 =A06.68 =A0 =A0 =A0 =A0 44.2
> Ala107 =A0 =A052.94 =A0 =A0 =A0 20.82 =A0 =A0 =A0 =A0 60.7
> Trp108 =A0 =A012.61 =A0 =A0 =A0 =A01.01 =A0 =A0 =A0 =A0 92.0
> Val109 =A0 =A082.20 =A0 =A0 =A0 68.19 =A0 =A0 =A0 =A0 17.0
> Residues losing more than 60% ASA on complex formation are in bold
>
> The accessible surface area (ASA) of the protein and the docked complex w=
ere
> calculated using NACCESS . The differences in =A0ASA of residues that are
> involved in ligand binding are
> calculated as ASAi =3D ASAi uncomplexed - ASAi complexed.
>
> These type of ASA calculation we have to =A0done our project, If you know=
 means
> please tell me the answer.
>
>
>
> -=3D This is automatically added to each message by the mailing script =
=3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt>
>
>


From owner-chemistry@ccl.net Wed Jul  1 14:32:01 2009
From: "M. Nicklaus mn1 .. helix.nih.gov" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: New NCI/CADD Web Services, incl. Standard InChIKey Resolver
Message-Id: <-39675-090701143018-29446-leObFShBSbY9zwCeM4+oxw#,#server.ccl.net>
X-Original-From: "M. Nicklaus" <mn1{:}helix.nih.gov>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Date: Wed, 1 Jul 2009 14:30:09 -0400 (Eastern Daylight Time)
MIME-Version: 1.0


Sent to CCL by: "M. Nicklaus" [mn1%%helix.nih.gov]
The NCI CADD Group is pleased to announce new or significantly upgraded web 
services and capabilities available at its web server http://cactus.nci.nih.gov.


Chemical Identifier Resolver (beta):
----------------------------
http://cactus.nci.nih.gov/chemical/structure

This service is a resolver for different chemical structure representations and 
identifiers, including those that do not carry any information about the 
structure itself. For instance, it can work as a Standard InChIKey Resolver, an 
NCI/CADD Identifier Resolver or a Chemical Name Resolver. The service also 
allows one to convert a given structure identifier into another representation 
or structure identifier.

Representations/identifiers supported are: Standard InChI/InChIKey, NCI/CADD 
Identifiers (FICuS, FICTS, uuuuu), SMILES, SDF, names, and a few other types of 
IDs.  See the web page for more information.

For those identifiers that require lookup, the underlying database currently 
contains about 67 million unique structure records, from which the respective 
Standard InChIKeys and NCI/CADD Identifiers have been calculated. For lookup by 
chemical names, 68 million names associated with 16 million unique structure 
records are currently available in the database. The database continues to grow.


Closely related are the new capabilities of resolving/converting chemical 
structure identifiers by simply using a URL adhering to the following scheme:
http://cactus.nci.nih.gov/chemical/structure/"structure identifier"/"representation"[/xml]

We just list a few examples here that should give you an idea of what's possible 
with this service.  For more detailed explanations, see the above web page.

Example: Standard InChI for chemical name string "aspirin":
http://cactus.nci.nih.gov/chemical/structure/aspirin/stdinchi

Example: Standard InChIKey of "ethanol" specified as SMILES string "CCO":
http://cactus.nci.nih.gov/chemical/structure/CCO/stdinchikey

Example: Unique SMILES string of chemical name string "benzene":
http://cactus.nci.nih.gov/chemical/structure/benzene/smiles

Example: SD File for chemical name string "morphine":
http://cactus.nci.nih.gov/chemical/structure/morphine/sdf

Example: Chemical names for Standard InChIKey "InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N" (Standard InChIKey of "ethanol"):
http://cactus.nci.nih.gov/chemical/structure/InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N/names

Example: Synonyms for chemical name string "aspirin":
http://cactus.nci.nih.gov/chemical/structure/aspirin/names



Optical Structure Recognition:
-----------------------------
http://cactus.nci.nih.gov/osra/

Converts graphical representations of chemical structures into SMILES. OSRA is 
available both as a downloadable open source code package and a simple web 
interface we've created on our server:

http://cactus.nci.nih.gov/cgi-bin/osra/index.cgi

The capabilities of OSRA have been substantially improved in the current 
version.



The NCI/CADD databases and web services team: Markus Sitzmann, Igor V. Filippov, Marc C. Nicklaus

------------------------------------------------------------------------
  Marc C. Nicklaus, Ph.D.                 NIH/NCI at Frederick
  E-mail: mn1(-)helix.nih.gov               Bldg 376, Rm 207
  Phone:  (301) 846-5903                  376 Boyles Street
  Fax:    (301) 846-6033                  FREDERICK, MD 21702      USA
             Head, Computer-Aided Drug Design (CADD) Group
      Laboratory of Medicinal Chemistry, Center for Cancer Research,
  National Cancer Institute at Frederick, National Institutes of Health
          http://ccr.cancer.gov/Staff/Staff.asp?profileid=6282
------------------------------------------------------------------------


From owner-chemistry@ccl.net Wed Jul  1 15:09:02 2009
From: "Vikash kumar kvikash01()gmail.com" <owner-chemistry#,#server.ccl.net>
To: CCL
Subject: CCL: Conformation search help
Message-Id: <-39676-090701043338-22037-WDkPbahUhko+qyysdXN49g#,#server.ccl.net>
X-Original-From: "Vikash kumar" <kvikash01-$-gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain;charset=utf-8
Date: Wed, 1 Jul 2009 13:03:17 +0530
MIME-Version: 1.0


Sent to CCL by: "Vikash kumar" [kvikash01|,|gmail.com]
Hi All

I want to know, is there any freely available Monte Carlo conformational
search for ligand like sucrose present on the web or not.

-- 
Thanks
With Regards

Biotechnology
School of Biosciences & Bioengg.
IIT Bombay
Powai
Mumbai-400076
India
Contact no. 09819442221


From owner-chemistry@ccl.net Wed Jul  1 15:41:00 2009
From: "Alessio Moriconi alessio.moriconi * dompe.it" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Pipeline pilot: chemical reaction .rxn
Message-Id: <-39677-090701114022-22674-XC+3ew/QZ+LMYx6S2jxCuQ^^server.ccl.net>
X-Original-From: "Alessio  Moriconi" <alessio.moriconi]^[dompe.it>
Date: Wed, 1 Jul 2009 11:40:18 -0400


Sent to CCL by: "Alessio  Moriconi" [alessio.moriconi-$-dompe.it]
Hi all,
I was wondering if any one would be able to help me.
I have a problem with an .rxn file containing a list of multiple and different reactions, in the form:

A  ->  B

I am using Pipeline Pilot 7.5 to manipulate this file. 
When I view the .rxn with an HTML molecular visualizer, for each reaction, some asterisks appear in several bonds (the reacting centers), generating a substructure. In the corresponding rxn file, these bonds (those highlighted by the asterisk) are flagged by 1, the others by 0 (last column), like:

$MOL

  -ISIS-  02010817122D

  5  4  0  0  0  0  0  0  0  0999 V2000
    3.4182   -3.4103    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
    2.7013   -2.1664    0.0000 O   0  0  0  0  0  0  0  0  0  3  0  0
    3.4182   -2.5809    0.0000 C   0  0  3  0  0  0  0  0  0  4  0  0
    1.9890   -2.5809    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
    4.1372   -2.1741    0.0000 O   0  0  0  0  0  0  0  0  0  8  0  0
  5  3  1  0  0  0  1
  2  4  1  0  0  0  0
  2  3  1  0  0  0  1
  3  1  1  0  0  0  0
M  END


I would like to write (canonical smiles) in a different file only these substructures in such a way for each reaction of the .rxn file.
Thanks for any help.

Alessio


From owner-chemistry@ccl.net Wed Jul  1 16:16:00 2009
From: "Babak Khalili khalili.babak\a/gmail.com" <owner-chemistry(0)server.ccl.net>
To: CCL
Subject: CCL: powerful Cocking software is required
Message-Id: <-39678-090701150740-15328-rzScLnB16JK1ng4xaeSNwg(0)server.ccl.net>
X-Original-From: Babak Khalili <khalili.babak!=!gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 1 Jul 2009 23:29:24 +0430
MIME-Version: 1.0


Sent to CCL by: Babak Khalili [khalili.babak##gmail.com]
Dear subscribers,

What is the best and powerful , free software to dock protein -protein
in windows? You will be so appreciated if introduce me.

Sincelerely,
Babak Khalili,
PhD Candidate of Biochemistry


From owner-chemistry@ccl.net Wed Jul  1 17:34:00 2009
From: "Wolf Ihlenfeldt wdi,xemistry.com" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Pipeline pilot: chemical reaction .rxn
Message-Id: <-39679-090701172936-16619-36J60Oh/S1tPiepZrCIv0Q]|[server.ccl.net>
X-Original-From: Wolf Ihlenfeldt <wdi%a%xemistry.com>
Content-Type: multipart/alternative; boundary=0016e6db66fafcb432046dab2cd0
Date: Wed, 1 Jul 2009 22:57:48 +0200
MIME-Version: 1.0


Sent to CCL by: Wolf Ihlenfeldt [wdi:xemistry.com]
--0016e6db66fafcb432046dab2cd0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 7bit

*I do not know about Pipeline Pilot, but this is of course straightforward
to script with Cactvs (www.xemistry.com):

filter create reactingbond property B_REACTION_CENTER value 0 operator !=
prop setparam X_SMILES unique 1
set fhout [molfile open "dompe.smi" w]
set fhin [molfile open "dompe.rxn"]
molfile loop $fhin xh {
    foreach eh [reaction ens $xh] {
        eval atom delete $eh [ens atoms $eh !reactingbond]
    }
    molfile write $fhout $xh
}
molfile close all

*
On Wed, Jul 1, 2009 at 5:40 PM, Alessio Moriconi alessio.moriconi * dompe.it
<owner-chemistry_._ccl.net> wrote:

>
> Sent to CCL by: "Alessio  Moriconi" [alessio.moriconi-$-dompe.it]
> Hi all,
> I was wondering if any one would be able to help me.
> I have a problem with an .rxn file containing a list of multiple and
> different reactions, in the form:
>
> A  ->  B
>
> I am using Pipeline Pilot 7.5 to manipulate this file.
> When I view the .rxn with an HTML molecular visualizer, for each reaction,
> some asterisks appear in several bonds (the reacting centers), generating a
> substructure. In the corresponding rxn file, these bonds (those highlighted
> by the asterisk) are flagged by 1, the others by 0 (last column), like:
>
> $MOL
>
>  -ISIS-  02010817122D
>
>  5  4  0  0  0  0  0  0  0  0999 V2000
>    3.4182   -3.4103    0.0000 C   0  0  0  0  0  0  0  0  0  1  0  0
>    2.7013   -2.1664    0.0000 O   0  0  0  0  0  0  0  0  0  3  0  0
>    3.4182   -2.5809    0.0000 C   0  0  3  0  0  0  0  0  0  4  0  0
>    1.9890   -2.5809    0.0000 C   0  0  0  0  0  0  0  0  0  6  0  0
>    4.1372   -2.1741    0.0000 O   0  0  0  0  0  0  0  0  0  8  0  0
>  5  3  1  0  0  0  1
>  2  4  1  0  0  0  0
>  2  3  1  0  0  0  1
>  3  1  1  0  0  0  0
> M  END
>
>
> I would like to write (canonical smiles) in a different file only these
> substructures in such a way for each reaction of the .rxn file.
> Thanks for any help.
>
> Alessio>
>
>

--0016e6db66fafcb432046dab2cd0
Content-Type: text/html; charset=UTF-8
Content-Transfer-Encoding: quoted-printable

<br><i>I do not know about Pipeline Pilot, but this is of course straightfo=
rward to script with Cactvs (<a href=3D"http://www.xemistry.com">www.xemist=
ry.com</a>):<br><br>filter create reactingbond property B_REACTION_CENTER v=
alue 0 operator !=3D<br>
prop setparam X_SMILES unique 1<br>set fhout [molfile open &quot;dompe.smi&=
quot; w]<br>set fhin [molfile open &quot;dompe.rxn&quot;]<br>molfile loop $=
fhin xh {<br>=C2=A0=C2=A0=C2=A0 foreach eh [reaction ens $xh] {<br>=C2=A0=
=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0=C2=A0 eval atom delete $eh [ens atoms $eh !r=
eactingbond]<br>
=C2=A0=C2=A0=C2=A0 }<br>=C2=A0=C2=A0=C2=A0 molfile write $fhout $xh<br>}<br=
>molfile close all<br><br></i><br><div class=3D"gmail_quote">On Wed, Jul 1,=
 2009 at 5:40 PM, Alessio Moriconi alessio.moriconi * <a href=3D"http://dom=
pe.it">dompe.it</a> <span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry=
_._ccl.net">owner-chemistry_._ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
Sent to CCL by: &quot;Alessio =C2=A0Moriconi&quot; [alessio.moriconi-$-<a h=
ref=3D"http://dompe.it" target=3D"_blank">dompe.it</a>]<br>
Hi all,<br>
I was wondering if any one would be able to help me.<br>
I have a problem with an .rxn file containing a list of multiple and differ=
ent reactions, in the form:<br>
<br>
A =C2=A0-&gt; =C2=A0B<br>
<br>
I am using Pipeline Pilot 7.5 to manipulate this file.<br>
When I view the .rxn with an HTML molecular visualizer, for each reaction, =
some asterisks appear in several bonds (the reacting centers), generating a=
 substructure. In the corresponding rxn file, these bonds (those highlighte=
d by the asterisk) are flagged by 1, the others by 0 (last column), like:<b=
r>

<br>
$MOL<br>
<br>
 =C2=A0-ISIS- =C2=A002010817122D<br>
<br>
 =C2=A05 =C2=A04 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =
=C2=A00999 V2000<br>
 =C2=A0 =C2=A03.4182 =C2=A0 -3.4103 =C2=A0 =C2=A00.0000 C =C2=A0 0 =C2=A00 =
=C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A01 =C2=A00 =C2=
=A00<br>
 =C2=A0 =C2=A02.7013 =C2=A0 -2.1664 =C2=A0 =C2=A00.0000 O =C2=A0 0 =C2=A00 =
=C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A03 =C2=A00 =C2=
=A00<br>
 =C2=A0 =C2=A03.4182 =C2=A0 -2.5809 =C2=A0 =C2=A00.0000 C =C2=A0 0 =C2=A00 =
=C2=A03 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A04 =C2=A00 =C2=
=A00<br>
 =C2=A0 =C2=A01.9890 =C2=A0 -2.5809 =C2=A0 =C2=A00.0000 C =C2=A0 0 =C2=A00 =
=C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A06 =C2=A00 =C2=
=A00<br>
 =C2=A0 =C2=A04.1372 =C2=A0 -2.1741 =C2=A0 =C2=A00.0000 O =C2=A0 0 =C2=A00 =
=C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A00 =C2=A08 =C2=A00 =C2=
=A00<br>
 =C2=A05 =C2=A03 =C2=A01 =C2=A00 =C2=A00 =C2=A00 =C2=A01<br>
 =C2=A02 =C2=A04 =C2=A01 =C2=A00 =C2=A00 =C2=A00 =C2=A00<br>
 =C2=A02 =C2=A03 =C2=A01 =C2=A00 =C2=A00 =C2=A00 =C2=A01<br>
 =C2=A03 =C2=A01 =C2=A01 =C2=A00 =C2=A00 =C2=A00 =C2=A00<br>
M =C2=A0END<br>
<br>
<br>
I would like to write (canonical smiles) in a different file only these sub=
structures in such a way for each reaction of the .rxn file.<br>
Thanks for any help.<br>
<br>
Alessio<br>
<br>
<br>
<br>
-=3D This is automatically added to each message by the mailing script =3D-=
<br<br=<br<br>
<br>
E-mail to subscribers: <a href=3D"mailto:CHEMISTRY_._ccl.net">CHEMISTRY_._ccl.n=
et</a> or use:<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
E-mail to administrators: <a href=3D"mailto:CHEMISTRY-REQUEST_._ccl.net">CHEM=
ISTRY-REQUEST_._ccl.net</a> or use<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/cgi-bin/ccl/send_ccl_mes=
sage" target=3D"_blank">http://www.ccl.net/cgi-bin/ccl/send_ccl_message</a>=
<br>
<br>
Subscribe/Unsubscribe:<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/chemistry/sub_unsub.shtm=
l" target=3D"_blank">http://www.ccl.net/chemistry/sub_unsub.shtml</a><br>
<br>
Before posting, check wait time at: <a href=3D"http://www.ccl.net" target=
=3D"_blank">http://www.ccl.net</a><br>
<br>
Job: <a href=3D"http://www.ccl.net/jobs" target=3D"_blank">http://www.ccl.n=
et/jobs</a><br>
Conferences: <a href=3D"http://server.ccl.net/chemistry/announcements/confe=
rences/" target=3D"_blank">http://server.ccl.net/chemistry/announcements/co=
nferences/</a><br>
<br>
Search Messages: <a href=3D"http://www.ccl.net/chemistry/searchccl/index.sh=
tml" target=3D"_blank">http://www.ccl.net/chemistry/searchccl/index.shtml</=
a><br>
<br<br>
 =C2=A0 =C2=A0 =C2=A0<a href=3D"http://www.ccl.net/spammers.txt" target=3D"=
_blank">http://www.ccl.net/spammers.txt</a><br>
<br>
RTFI: <a href=3D"http://www.ccl.net/chemistry/aboutccl/instructions/" targe=
t=3D"_blank">http://www.ccl.net/chemistry/aboutccl/instructions/</a><br>
<br>
<br>
</blockquote></div><br>

--0016e6db66fafcb432046dab2cd0--


From owner-chemistry@ccl.net Wed Jul  1 18:08:01 2009
From: "Bryan Bishop kanzure(0)gmail.com" <owner-chemistry{:}server.ccl.net>
To: CCL
Subject: CCL: Pipeline pilot: chemical reaction .rxn
Message-Id: <-39680-090701171818-15826-FJWZI1aTdbEjVGPzaO0pJQ{:}server.ccl.net>
X-Original-From: Bryan Bishop <kanzure+*+gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=ISO-8859-1
Date: Wed, 1 Jul 2009 15:48:57 -0500
MIME-Version: 1.0


Sent to CCL by: Bryan Bishop [kanzure|-|gmail.com]
On Wed, Jul 1, 2009 at 10:40 AM, Alessio Moriconi alessio.moriconi *
dompe.it wrote:
> I am using Pipeline Pilot 7.5 to manipulate this file.
> When I view the .rxn with an HTML molecular visualizer, for each reaction, some asterisks appear in several bonds (the reacting

Hello, I was wondering if you know of any other software to play
around with dot RXN files. It sounds very interesting, but I have
never heard of this format. Thank you,

- Bryan
http://heybryan.org/
1 512 203 0507


From owner-chemistry@ccl.net Wed Jul  1 23:30:01 2009
From: "Nestor J Cubillan njca12(_)gmail.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: Perl and unformatted checkpoint files of gaussian
Message-Id: <-39681-090701231956-29922-WoMYcoEwn/qIriXhAHGkhg() server.ccl.net>
X-Original-From: "Nestor J Cubillan" <njca12 ~~ gmail.com>
Date: Wed, 1 Jul 2009 23:19:52 -0400


Sent to CCL by: "Nestor J Cubillan" [njca12^_^gmail.com]
Hi *,
 

Is there any perl script to extract data (e.g. total energy) from an unformatted checkpoint file of Gaussian?

Thanks in advances

Nestor