From owner-chemistry@ccl.net Wed Feb 18 00:21:01 2009 From: "Benjamin Roberts benjamincharlesroberts ~ gmail.com" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38646-090217205631-13472-2KYSnAY6tVkvN02Yhy2zYw%x%server.ccl.net> X-Original-From: Benjamin Roberts Content-Type: multipart/alternative; boundary=000e0cd15534b50b58046327b916 Date: Wed, 18 Feb 2009 10:56:17 +0900 MIME-Version: 1.0 Sent to CCL by: Benjamin Roberts [benjamincharlesroberts##gmail.com] --000e0cd15534b50b58046327b916 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit The gromacs directory containing the configure script should be wherever you unpacked the tarball, unless you specified elsewhere when you unpacked it. The /usr/local/gromacs directory would only be created when you run # make install, which comes after you configure and compile. Try reading $ man tar or googling to see how it works.Ben On Wed, Feb 18, 2009 at 7:03 AM, Maura Mooney mmooney05#,#qub.ac.uk < owner-chemistry=-=ccl.net> wrote: > > Sent to CCL by: "Maura Mooney" [mmooney05|*|qub.ac.uk] > I have tried this, and it does seem to work but I still cant locate the > gromacs directory, which should i think be in /usr/local/gromacs. > > Any suggestions? > > Thanx, > > M > > > "Ted Cabeen cabeen]|[chem.ucsb.edu" wrote: > > > > Sent to CCL by: Ted Cabeen [cabeen[]chem.ucsb.edu] > > You need to untar the file that gunzip created. You should now have a > > file called fftw3....tar. Run tar xvf fftw3....tar and it will extract > > what you need. > > > > In the future, you can do this in one step by adding the z flag to tar > > and just running tar xvzf fftw3...tar.gz. > > > > --Ted > > > > Maura Mooney mmooney05()qub.ac.uk wrote: > > > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > > > Hi all, > > > > > > I am having problem configuring gromacs on my dell machine. I have > unzipped the gromacs archive and also the fftw3...tar.gz file (required as a > prerequisite). The next step requires > > > > > > cd to the gromacs directory and ./configure. > > > > > > But I can't seem to locate the gromacs directory, or the configure > program, thus I cannot go any further with the configuration/installation. > > > > > > The installation appears quite difficult...Can anyone help? :( > > > > > > Thanx, > > > > > > M> > > --000e0cd15534b50b58046327b916 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable The gromacs directory containing the configure script should be wherever yo= u unpacked the tarball, unless you specified elsewhere when you unpacked it= . The /usr/local/gromacs directory would only be created when you run # mak= e install, which comes after you configure and compile. Try reading $ man t= ar or googling to see how it works.
Ben

On Wed, Feb 18, 2009 at 7:03 AM, Maur= a Mooney mmooney05#,#qub.ac.uk <owner-chemistry=-=ccl= .net> wrote:

Sent to CCL by: "Maura  Mooney" [mmooney05|*|qub.ac.uk]
I have tried this, and it does seem to work but I still cant locate the gro= macs directory, which should i think be in /usr/local/gromacs.

Any suggestions?

Thanx,

M

> "Ted Cabeen cabeen]|[chem.ucsb.edu"  wrote:
>
> Sent to CCL by: Ted Cabeen [cabeen[]chem.ucsb.edu]
> You need to untar the file that gunzip created.  You should now h= ave a
> file called fftw3....tar.  Run tar xvf fftw3....tar and it will e= xtract
> what you need.
>
> In the future, you can do this in one step by adding the z flag to tar=
> and just running tar xvzf fftw3...tar.gz.
>
> --Ted
>
> Maura Mooney mmooney05()qub.ac.uk wrote:
> > Sent to CCL by: "Maura  Mooney" [mmooney05::qub.ac.uk]
> > Hi all,
> >
> > I am having problem configuring gromacs on my dell machine. I hav= e unzipped the gromacs archive and also the fftw3...tar.gz file (required a= s a prerequisite). The next step requires
> >
> > cd to the gromacs directory and ./configure.
> >
> > But I can't seem to locate the gromacs directory, or the conf= igure program, thus I cannot go any further with the configuration/installa= tion.
> >
> > The installation appears quite difficult...Can anyone help? :( > >
> > Thanx,
> >
> > M>
> >
>
>



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--000e0cd15534b50b58046327b916-- From owner-chemistry@ccl.net Wed Feb 18 02:13:00 2009 From: "Peter Schmidtke pschmidtke]_[mmb.pcb.ub.es" To: CCL Subject: CCL: Gromacs installation on Dell Ubuntu Message-Id: <-38647-090217154119-6320-0+AbhS9wttQ/mlzuVX9k4Q=server.ccl.net> X-Original-From: Peter Schmidtke Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="UTF-8" Date: Tue, 17 Feb 2009 21:04:48 +0100 MIME-Version: 1.0 Sent to CCL by: Peter Schmidtke [pschmidtke[]mmb.pcb.ub.es] Gromacs is, to my knowledge, contained in the Synaptic Package Manager available in Ubuntu. Thus installing Gromacs using "apt-get install gromacs" should install and configure everything automatically. Try this first, and afterwards "manual" configuration. On Tue, 17 Feb 2009 09:24:18 -0800 (PST), "Loan Huynh huynhkl2000]*[yahoo.ca" wrote: > You should go to Gromacs mailing list. I'm sure that there are many > advice posted already on that list. Here is the link: > http://www.gromacs.org/component/option,com_wrapper/Itemid,165/ >=20 > --- On Tue, 2/17/09, Maura Mooney mmooney05()qub.ac.uk > wrote: >> From: Maura Mooney mmooney05()qub.ac.uk > Subject: CCL: Gromacs installation on Dell Ubuntu > To: "Huynh, Loan " > Received: Tuesday, February 17, 2009, 11:35 AM >=20 > Sent to CCL by: "Maura Mooney" [mmooney05::qub.ac.uk] > Hi all, >=20 > I am having problem configuring gromacs on my dell machine. I have unzipped > the > gromacs archive and also the fftw3...tar.gz file (required as a > prerequisite). > The next step requires >=20 > cd to the gromacs directory and ./configure. >=20 > But I can't seem to locate the gromacs directory, or the configure program, > thus I cannot go any further with the configuration/installation. >=20 > The installation appears quite difficult...Can anyone help? :( >=20 > Thanx, >=20 > M >=20 >=20 >=20 > -=3D This is automatically added to each message by the mailing script > =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscrib= e:http://www.ccl.net/spammers.txt >=20 >=20 > _________________________________________________________________= _ > Yahoo! Canada Toolbar: Search from anywhere on the web, and bookmark yo= ur > favourite sites. Download it now at > http://ca.toolbar.yahoo.com. --=20 Peter Schmidtke ---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona From owner-chemistry@ccl.net Wed Feb 18 04:13:00 2009 From: "Hatice Can alphacan2000##yahoo.com" To: CCL Subject: CCL: Verloop's sterimol descriptors Message-Id: <-38648-090217105053-10210-biu6mXxyruqyiyLnuwqQDw!^!server.ccl.net> X-Original-From: Hatice Can Content-Type: multipart/alternative; boundary="0-670930562-1234882238=:15661" Date: Tue, 17 Feb 2009 06:50:38 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Hatice Can [alphacan2000===yahoo.com] --0-670930562-1234882238=:15661 Content-Type: text/plain; charset=us-ascii Dear CCLers, I need to calculate Verloop's sterimol descriptors of some compounds. If you could give some direction how I can calculate them, I will be appreciated. many thanks and regards hatice --0-670930562-1234882238=:15661 Content-Type: text/html; charset=us-ascii
Dear CCLers,
 
I need to calculate Verloop's sterimol descriptors of some compounds. If you could give some direction how I can calculate them, I will be appreciated.
 
many thanks and regards
 
hatice

--0-670930562-1234882238=:15661-- From owner-chemistry@ccl.net Wed Feb 18 08:50:01 2009 From: "David Cornil cornildavid^yahoo.fr" To: CCL Subject: CCL: k point mesh Message-Id: <-38649-090218084545-10362-Yxw+TbICoolYACzTpYLSPQ\a/server.ccl.net> X-Original-From: "David Cornil" Date: Wed, 18 Feb 2009 08:45:41 -0500 Sent to CCL by: "David Cornil" [cornildavid()yahoo.fr] Dear CCL'users I have a question about the number of k point we need to perform a calculation in periodic boundary conditions of specific systems like [metalic electrode]-[molecule]-[metalic electrode] with molecule along the z axis. Some litteratures mention k point parameters around 1x1x100 or 3x3x100 for Brillouin zone integration. It surprising me because in interface system like SAM in periodic condition k point parameters are like 8x8x1. Can you explain to me the reasons of this difference ? Thank you in advance David A. M. Cornil Ph.D Student University of Mons-Hainaut Belgium From owner-chemistry@ccl.net Wed Feb 18 09:24:01 2009 From: "ramesh kumar arumugam rame_sh_kum!^!yahoo.co.in" To: CCL Subject: CCL: how to use scan in ADF Message-Id: <-38650-090218060939-30595-1lXP93zWATjWcqWbiIZ5WA##server.ccl.net> X-Original-From: "ramesh kumar arumugam" Date: Wed, 18 Feb 2009 06:09:35 -0500 Sent to CCL by: "ramesh kumar arumugam" [rame_sh_kum|*|yahoo.co.in] I am new to use ADF.I dont know how to use scan option in ADF.can any one suggest me with an example? A.Rameshkumar rame_sh_kum : yahoo.co.in From owner-chemistry@ccl.net Wed Feb 18 10:01:00 2009 From: "ramesh kumar rame_sh_kum..yahoo.co.in" To: CCL Subject: CCL: how to use scan in ADF Message-Id: <-38651-090218072530-3627-Xon7r69pDpi2ERfdZnr/yg#%#server.ccl.net> X-Original-From: ramesh kumar Content-Type: multipart/alternative; boundary="0-913534276-1234956227=:950" Date: Wed, 18 Feb 2009 16:53:47 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: ramesh kumar [rame_sh_kum^yahoo.co.in] --0-913534276-1234956227=:950 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable I am new to use ADF, I dont know how to use scan in ADF. Can any one suggest me how=C2=A0to do it with an example? =C2=A0 =C2=A0 =C2=A0 A.Rameshkumar Mail: rame_sh_kum~!~yahoo.co.in=C2=A0=0A=0A=0A Add more friends to your = messenger and enjoy! Go to http://messenger.yahoo.com/invite/ --0-913534276-1234956227=:950 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable

I am new to use ADF, I dont know how to= use scan in ADF.
Can any one suggest me how to do it with an example?
 
 
 
A.Rameshkumar
Mail: rame_sh_kum~!~yahoo.co.in 

=0A =
Add more friends to your messenger and enjoy! = Invite them now. --0-913534276-1234956227=:950-- From owner-chemistry@ccl.net Wed Feb 18 10:35:00 2009 From: "Marcel Swart marcel.swart|*|icrea.es" To: CCL Subject: CCL: how to use scan in ADF Message-Id: <-38652-090218101807-20739-8p3/62L4ZFLtKBdTWfs0pA+/-server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-35--1034968245 Date: Wed, 18 Feb 2009 16:17:49 +0100 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart a icrea.es] --Apple-Mail-35--1034968245 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed See for instance: http://www.scm.com/Doc/Doc2008.01/ADF/Examples/page45.html On Feb 18, 2009, at 12:09 PM, ramesh kumar arumugam rame_sh_kum!^!=20 yahoo.co.in wrote: > > Sent to CCL by: "ramesh kumar arumugam" [rame_sh_kum|*|yahoo.co.in] > I am new to use ADF.I dont know how to use scan option in ADF.can =20 > any one suggest me with an example? > > > > A.Rameshkumar > rame_sh_kum^^yahoo.co.in =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart|,|icrea.es marcel.swart|,|udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-35--1034968245 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

See for instance:


On Feb 18, 2009, at 12:09 PM, ramesh kumar arumugam = rame_sh_kum!^!yahoo.co.in wrote:


Sent to = CCL by: "ramesh kumar arumugam" [rame_sh_kum|*|yahoo.co.in]
I am new to use ADF.I dont know how to use scan = option in ADF.can any one suggest me with an example?



A.Rameshkumar
dr. Marcel = Swart

ICREA = researcher=A0at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
17003 Girona
Catalunya = (Spain)

tel
marcel.swart|,|udg.edu



=

= --Apple-Mail-35--1034968245-- From owner-chemistry@ccl.net Wed Feb 18 12:30:01 2009 From: "chezbowlus+*+comcast.net" To: CCL Subject: CCL: Verloop's sterimol descriptors Message-Id: <-38653-090218112046-31039-Gg8xW40bhMdebL2AiQ5nfg#%#server.ccl.net> X-Original-From: chezbowlus|a|comcast.net Content-Type: multipart/alternative; boundary="----=_Part_49359_1328905195.1234972062424" Date: Wed, 18 Feb 2009 15:47:42 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: chezbowlus*|*comcast.net ------=_Part_49359_1328905195.1234972062424 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable There are several variants of this available, and included in several descr= iptor generation packages.=C2=A0 Take a look at what may be available throu= gh Sybyl, MOE, or Dragon, to mention only a few.=20 The original program is/was available through QCPE since about 1994, but I = don't know if QCPE is still in operation.=C2=A0 I've distributed personal c= opies here and there; perhaps one of the recipients may be able to send you= workable code.=20 I deposited some documentation=C2=A0at the CCL site. I don't recall I have = the program itself in electronic form, but I'm pretty sure I still have the= listing, in an ancient FORTRAN dialect.=20 Cheers,=20 Steve Bowlus=20 ----- Original Message -----=20 > From: "Hatice Can alphacan2000##yahoo.com" =20 To: "Steve Bowlus" =20 Sent: Tuesday, February 17, 2009 6:50:38 AM GMT -08:00 US/Canada Pacific=20 Subject: CCL: Verloop's sterimol descriptors=20 Dear CCLers,=20 I need to calculate Verloop's sterimol descriptors of some compounds. If yo= u could give some direction how I can calculate them, I will be appreciated= .=20 many thanks and regards=20 hatice=20 =C2=A0=C2=A0 =C2=A0 =C2=A0 ------=_Part_49359_1328905195.1234972062424 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 7bit

There are several variants of this available, and included in several descriptor generation packages.  Take a look at what may be available through Sybyl, MOE, or Dragon, to mention only a few.

 

The original program is/was available through QCPE since about 1994, but I don't know if QCPE is still in operation.  I've distributed personal copies here and there; perhaps one of the recipients may be able to send you workable code.

 

I deposited some documentation at the CCL site. I don't recall I have the program itself in electronic form, but I'm pretty sure I still have the listing, in an ancient FORTRAN dialect.

 

Cheers,

Steve Bowlus

 

 


----- Original Message -----
From: "Hatice Can alphacan2000##yahoo.com" <owner-chemistry]-[ccl.net>
To: "Steve Bowlus" <chezbowlus]-[comcast.net>
Sent: Tuesday, February 17, 2009 6:50:38 AM GMT -08:00 US/Canada Pacific
Subject: CCL: Verloop's sterimol descriptors

Dear CCLers,

I need to calculate Verloop's sterimol descriptors of some compounds. If you could give some direction how I can calculate them, I will be appreciated.

many thanks and regards

hatice


      

------=_Part_49359_1328905195.1234972062424-- From owner-chemistry@ccl.net Wed Feb 18 14:03:01 2009 From: "Reaz Uddin riaasuddin^-^yahoo.com" To: CCL Subject: CCL: atom types Message-Id: <-38654-090218030119-7137-6WBRAxGtVDVbvQBq6r8HcA*_*server.ccl.net> X-Original-From: Reaz Uddin Content-Type: multipart/alternative; boundary="0-2093772464-1234940464=:98261" Date: Tue, 17 Feb 2009 23:01:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Reaz Uddin [riaasuddin],[yahoo.com] --0-2093772464-1234940464=:98261 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi Folks, I was just wondering what should be the atom types of each Nitrogen in Azid= e group (R-N=3DN+=3DN-=A0) in Sybyl or any common molecular operating progr= ams ?? Thank you so much for your time. REAZUDDIN=20 Research Scholar=20 HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin*yahoo.com, mriazuddin*iccs.edu=0A=0A=0A --0-2093772464-1234940464=:98261 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Folks,
I was just wondering what should be the atom typ= es of each Nitrogen in Azide group (R-N= =3DN+=3DN- = ;) in Sybyl or any common molecular operating programs ??
Thank you so much for your time.

<= SPAN style=3D"COLOR: rgb(0,0,127)">REAZUDDIN
Research Scholar
HEJ Resea= rch Institute of Chemistry
Univ= ersity of Karachi
Karachi, Pakistan
Email: riaasuddin*yahoo.com, mriazuddin*iccs.edu<= /A>

=0A=0A --0-2093772464-1234940464=:98261-- From owner-chemistry@ccl.net Wed Feb 18 14:41:00 2009 From: "Bob Clark bclark::bcmetrics.com" To: CCL Subject: CCL: Verloop's sterimol descriptors Message-Id: <-38655-090218143936-10256-TTv3DcpCgZwBb8M8qdVVzQ{:}server.ccl.net> X-Original-From: Bob Clark Content-Type: multipart/mixed; boundary="------------070204000604010307040305" Date: Wed, 18 Feb 2009 13:39:19 -0600 MIME-Version: 1.0 Sent to CCL by: Bob Clark [bclark%a%bcmetrics.com] This is a multi-part message in MIME format. --------------070204000604010307040305 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
A. Verloop & J. Tipker.   Use of linear free energy related and other parameters in the study of fungicidal selectivity.  Pesticide Science 1976, 7 (4), 379 - 390.

Hatice Can alphacan2000##yahoo.com wrote:
Dear CCLers,
 
I need to calculate Verloop's sterimol descriptors of some compounds. If you could give some direction how I can calculate them, I will be appreciated.
 
many thanks and regards
 
hatice

--------------070204000604010307040305 Content-Type: text/x-vcard; charset=utf-8; name="bclark.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="bclark.vcf" begin:vcard fn:Robert D. Clark n:Clark;Robert D. org:Biochemical Infometrics adr:;;827 Renee Lane;St. Louis;MO;63141;USA email;internet:bclark[#]bcmetrics.com title:Founder & Chief Scientist tel;work:+1-314-660-4499 tel;cell:+1-314-660-4499 x-mozilla-html:TRUE url:http://www.bcmetrics.com version:2.1 end:vcard --------------070204000604010307040305-- From owner-chemistry@ccl.net Wed Feb 18 15:17:01 2009 From: "Tamas Gunda tgunda1 .. puma.unideb.hu" To: CCL Subject: CCL: Verloop's sterimol descriptors Message-Id: <-38656-090218102549-25115-/UGctulQn66/ppCb8S6C+Q:_:server.ccl.net> X-Original-From: "Tamas Gunda" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0033_01C991E0.5BFC8F30" Date: Wed, 18 Feb 2009 15:48:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda1#puma.unideb.hu] This is a multi-part message in MIME format. ------=_NextPart_000_0033_01C991E0.5BFC8F30 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Mol2mol can calculate them. You need any common molecule file of the = compound, and after inputting it into Mol2mol you have to mark the = joining bond (as Verloop's procedure regards the molecule as a = substituent) http://www.gunda.hu/mol2mol Tamas Gunda ----- Original Message -----=20 From: Hatice Can alphacan2000##yahoo.com=20 To: Gunda, Tamas E =20 Sent: Tuesday, February 17, 2009 15:50 PM Subject: CCL: Verloop's sterimol descriptors Dear CCLers, I need to calculate Verloop's sterimol descriptors of some compounds. = If you could give some direction how I can calculate them, I will be = appreciated.=20 many thanks and regards hatice ------=_NextPart_000_0033_01C991E0.5BFC8F30 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Mol2mol can calculate them. You need any common = molecule file=20 of the compound, and after inputting it into Mol2mol you have to = mark the=20 joining bond (as Verloop's procedure regards the molecule as a=20 substituent)
 
http://www.gunda.hu/mol2mol
 
Tamas Gunda
----- Original Message -----
From:=20 Hatice=20 Can alphacan2000##yahoo.com
Sent: Tuesday, February 17, = 2009 15:50=20 PM
Subject: CCL: Verloop's = sterimol=20 descriptors

Dear CCLers,
 
I need to calculate Verloop's sterimol descriptors of some = compounds. If=20 you could give some direction how I can calculate them, I will be = appreciated.=20
 
many thanks and regards
 
hatice

------=_NextPart_000_0033_01C991E0.5BFC8F30-- From owner-chemistry@ccl.net Wed Feb 18 20:04:00 2009 From: "Wayne Steinmetz WES04747:_:pomona.edu" To: CCL Subject: CCL: atom types Message-Id: <-38657-090218164043-17660-bW6JjoDBkj5OLFDO+W9qJQ * server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C9920C.B640C789" Date: Wed, 18 Feb 2009 13:06:02 -0800 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747__pomona.edu] This is a multi-part message in MIME format. ------_=_NextPart_001_01C9920C.B640C789 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable SYBYL's sketch module allows one to construct a molecule using substituents and fortunately the azide group is on the list. =20 Here is the atom typing in brackets for each heavy atom in methylazide (H3CNNN): C[C3]N[N2]N[N1]N[N2] . =20 Wayne E. Steinmetz=20 Professor Emeritus of Chemistry=20 USFS Volunteer=20 Chemistry Department=20 Pomona College=20 645 North College Avenue=20 Claremont, California 91711-6338=20 USA=20 phone: 1-909-621-8447=20 FAX: 1-909-607-7726=20 Email: wsteinmetz(0)pomona.edu=20 WWW: pages.pomona.edu/~wsteinmetz=20 =20 ________________________________ > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu(0)ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu(0)ccl.net] On Behalf Of Reaz Uddin riaasuddin^-^yahoo.com Sent: Tuesday, February 17, 2009 11:01 PM To: Wayne Steinmetz Subject: CCL: atom types =20 Hi Folks, I was just wondering what should be the atom types of each Nitrogen in Azide group (R-N=3DN+=3DN- ) in Sybyl or any common molecular operating programs ?? Thank you so much for your time. REAZUDDIN=20 Research Scholar=20 HEJ Research Institute of Chemistry University of Karachi Karachi, Pakistan Email: riaasuddin=3Dyahoo.com, mriazuddin=3Diccs.edu =20 ------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D ------_=_NextPart_001_01C9920C.B640C789 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

SYBYL’s sketch module allows = one to construct a molecule using substituents and fortunately the azide group = is on the list.

 

Here is the atom typing in brackets = for each heavy atom in methylazide (H3CNNN): C[C3]N[N2]N[N1]N[N2] = .

 

Wayne E. Steinmetz
Professor Emeritus of Chemistry
USFS Volunteer
Chemistry Department
Pomona College
645 North College Avenue
Claremont, California 91711-6338
USA
phone: 1-909-621-8447
FAX: 1-909-607-7726
Email: wsteinmetz(0)pomona.edu
WWW: pages.pomona.edu/~wsteinmetz
 

From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu(0)ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu(0)ccl.net] = On Behalf Of Reaz Uddin riaasuddin^-^yahoo.com
Sent: Tuesday, February = 17, 2009 11:01 PM
To: Wayne Steinmetz
Subject: CCL: atom = types

 

Hi = Folks,

I was just wondering what = should be the atom types of each Nitrogen in Azide group = (R-N=3DN+=3DN- ) in Sybyl or any common molecular operating programs = ??

Thank you so much for your = time.

REAZUDDIN
Research Scholar
HEJ Research Institute of Chemistry
University of Karachi
Karachi, = Pakistan
Email: riaasuddin=3Dyahoo.com, mriazuddin=3Diccs.edu

 

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