From owner-chemistry@ccl.net Sat Apr 15 11:23:00 2006 From: "Dr. N. SUKUMAR nagams]|[rpi.edu" To: CCL Subject: CCL:G: Cube file Message-Id: <-31519-060414104008-1216-+DaUbu0hRhIbMC+bKOHl2g!=!server.ccl.net> X-Original-From: "Dr. N. SUKUMAR" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Fri, 14 Apr 2006 10:40:07 -0400 MIME-Version: 1.0 Sent to CCL by: "Dr. N. SUKUMAR" [nagams-$-rpi.edu] ==============Original message text=============== On Thu, 13 Apr 2006 10:14:50 EDT "Ricky Shen hxhgxy2:_:163.com" wrote: Sent to CCL by: "Ricky Shen" [hxhgxy2++163.com] Hi, Only Computing the Laplacian of the density, The error will be appear. the cube file can't be archived. My input file: %rwf=csc,-1 %nosave %chk=csc %mem=750mb P b3lyp/6-31g* geom=check guess=read Cube=(laplacian,Fine) No title specified 0 1 csc.cube And the error: PGFIO-F-217/formatted read/unit=5/attempt to read past end of file. File name = /home/swain/sc/Gau-3661.inp formatted, sequential access record = 12 In source file dencub.f, at line number 366 At Linux OS, both G98 and G03 have error, but it not appear at Windows OS. ===========End of original message text=========== Could be a dos2unix problem. Do you have an end-of-line character (or a blank line) after the laat line? Dr. N. Sukumar Center for Biotechnology and Interdisciplinary Studies Rensselaer Polytechnic Institute From owner-chemistry@ccl.net Sat Apr 15 11:57:02 2006 From: "Michael K. Gilson gilson .. umbi.umd.edu" To: CCL Subject: CCL: Database for HIV protease inhibitors Message-Id: <-31520-060415113753-22231-CdhhrkCwzeqZgrFqLyiwUQ-.-server.ccl.net> X-Original-From: "Michael K. Gilson" Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Sat, 15 Apr 2006 10:34:08 -0400 MIME-version: 1.0 Sent to CCL by: "Michael K. Gilson" [gilson~~umbi.umd.edu] You can download chemical structures and inhibition data for nearly 2000 HIV protease inhibition studies from BindingDB, www.bindingdb.org Use the pulldown target list to select HIV-1 protease, and you'll find there are around 1800 enzyme inhibition data. Hit the Search button for the enzyme inhibition data and you'll go to a data summary table. You can then download ALL the data as an SDfile if you click the "Add all pages" at the top of the table then "Make Data Set". You'll need to register as a BindingDB user, and then you'll be able to download the SDfile. Best regards, Mike If you choose "Target Names" on the left-hand side of the M. Nicklaus mn1::helix.nih.gov wrote: >Sent to CCL by: "M. Nicklaus" [mn1 ~ helix.nih.gov] >Have you tried the HIV / OI / TB Therapeutics Database at >http://chemdb.niaid.nih.gov/struct_search/default.html ? > >Marc Nicklaus > > >On Wed, 12 Apr 2006, jz7:+:duke.edu wrote: > > > >>Sent to CCL by: jz7|duke.edu >>Dear all, >> >>I am working on a course project about HIV protease inhibitors. Does >>anyone know where I can find the data set (structural, charge, and >>bio-activity imformation) for HIV protease inhibitors? >> >>Really appreciate the help!> > > > > -- Michael K. Gilson, M.D., Ph.D. CARB Fellow and Professor Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute 9600 Gudelsky Drive Rockville, MD 20850 Voice: 240-314-6217 Fax: 240-314-6255 gilsonumbi.umd.edu From owner-chemistry@ccl.net Sat Apr 15 14:48:00 2006 From: "Om ompandey###gmail.com" To: CCL Subject: CCL: software to convert name into structure Message-Id: <-31521-060415015525-10361-I7ERdm8Tg5RABN2QG4IwUA*_*server.ccl.net> X-Original-From: Om Content-Type: multipart/alternative; boundary="----=_Part_35141_6587170.1145076642874" Date: Sat, 15 Apr 2006 10:20:42 +0530 MIME-Version: 1.0 Sent to CCL by: Om [ompandey]-[gmail.com] ------=_Part_35141_6587170.1145076642874 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, Lexichem, from Open Eye (Academic-free), provides efficient conversion of chemical names to chemical structures and vice versa, where chemical names can be standard IUPAC names or more common traditional names, while Lexichem's companion product, Ogham, provides useful 2D renderings. More information: http://www.eyesopen.com/products/toolkits/lexichem.html Hope this helps Om Prakash, Research Student Bioinformatics Center, University of Pune, Pune-411007 India On 4/1/06, Shireen Alfalah shireen.alfalah * yahoo.com < owner-chemistry*|*ccl.net> wrote: > > Sent to CCL by: Shireen Alfalah [shireen.alfalah ~ yahoo.com] > --0-1568940659-1143909564=3D:75530 > Content-Type: text/plain; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear CCL users, > I am wondering if there is a free software that can convert the name of a > compound into chemical structure. I am aware of the pubchem but it just > gives the structure in image format. I am wondering if there is a free > software that can convert the name into structure with a format that > hyperchem (for example) or any other molecular building software can read= . > > Thanks in advance. > > > > > > ************************************** > Sherin Alfalah > PhD Student > Theoretical Chemist > Chemistry Department > AlQuds University > ************************************** > > --------------------------------- > New Yahoo! Messenger with Voice. Call regular phones from your PC and sav= e > big. > --0-1568940659-1143909564=3D:75530 > Content-Type: text/html; charset=3Diso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear CCL users,
I am wondering if there is a free > software that can convert the name of a compound into chemical structure.= I > am aware of the pubchem but it just gives the structure in image format. = I > am wondering if there is a free software that can convert the name into > structure with a format that hyperchem (for example) or any oth= er > molecular building software can read.
 
Than= ks > in advance. >
 
 
 


**= ************************************ >
Sherin Alfalah
PhD Student
Theoretical Chemist
Chemistry > Department
AlQuds University >
**************************************

>

New Yahoo! Messenger with Voice. http://us.rd.yahoo.com/mail_us/taglines/postman5/*http://us.rd.yahoo.com/= evt=3D39666/*http://beta.messenger.yahoo.com">Call > regular phones from your PC and save big. > --0-1568940659-1143909564=3D:75530-- > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > > -- Om Prakash Research Student, Bioinformatics Center University of Pune Pune-411007 India ------=_Part_35141_6587170.1145076642874 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi,

 

Lexichem, from Open Eye (Academic-free), provides efficient conversion of= chemical names to chemical structures and vice versa, where chemical names= can be standard IUPAC names or more common traditional names, while Lexich= em's companion product, Ogham, provides useful 2D renderings.

 

More information:

 

http://www.eyesopen.com/products/toolkits/lexichem.html

 

Hope this helps

 

Om Prakash,

Research Student

Bioinformatics Center,

University of Pune,

Pune-411007

India



 
On 4/1/06, S= hireen Alfalah shireen.alfalah * yahoo.com= <owner-chemistry*|*ccl.net= > wrote:
Sent to CCL by: Shireen Alfalah = [shireen.alfalah ~ yahoo.com]
--0-15689= 40659-1143909564=3D:75530
Content-Type: text/plain; charset=3Diso-8859-1
Content-Transfer-Enco= ding: 8bit

Dear CCL users,
I am wondering if there is a free soft= ware that can convert the name of a compound into chemical structure. I am = aware of the pubchem but it just gives the structure in image format. I am = wondering if there is a free software that can convert the name into struct= ure with a format that hyperchem (for example) or any other molecular build= ing software can read.

Thanks in advance.





*************************= *************
Sherin Alfalah
PhD Student
Theoretical Chemist
Ch= emistry Department
AlQuds University
********************************= ******

---------------------------------
New Yahoo! Messenger with Voic= e. Call regular phones from your PC and save big.
--0-1568940659-1143909= 564=3D:75530
Content-Type: text/html; charset=3Diso-8859-1
Content-Tr= ansfer-Encoding: 8bit

<DIV>Dear CCL users,</DIV>  <DIV>I am w= ondering if there is a free software that can convert the name of a compoun= d into chemical structure. I am aware of the pubchem but it just gives the = structure in image format. I am wondering if there is a free software that = can convert the name into structure&nbsp;with a format that hyperchem (= for example)&nbsp;or any other molecular building software can read.<= ;/DIV>  <DIV>&nbsp;</DIV>  <DIV&g= t;Thanks in advance. </DIV>  <DIV>&nbsp;</DIV&= gt;  <DIV>&nbsp;</DIV>  <DIV>&= ;nbsp;</DIV><BR><BR>*************************************= * <BR>Sherin Alfalah <BR>PhD Student <BR>Theoretical Chem= ist <BR>Chemistry Department <BR>AlQuds University <BR>**= ************************************<p>
            = ;   <hr size=3D1>New Yahoo! Messenger with Voice. <a hre= f=3D"http://us.= rd.yahoo.com/mail_us/taglines/postman5/*http://us.rd.yahoo.com/evt=3D39666/= *http://beta.messenger.yahoo.com ">Call regular phones from your PC</a> and save big.
-= -0-1568940659-1143909564=3D:75530--



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-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-= +-+-+-+-+






-- Om Prakash
Research Student,
Bioinformatics Center
University of= Pune
Pune-411007
India=20 ------=_Part_35141_6587170.1145076642874--