From owner-chemistry@ccl.net Wed Dec 30 09:45:01 2009 From: "Sangeetha Subramaniam srdshigella]~[gmail.com" To: CCL Subject: CCL: Data processing before descriptor calculation Message-Id: <-40978-091230011632-20558-6b+P/mbCMAU+jTA7HBNePg!A!server.ccl.net> X-Original-From: "Sangeetha Subramaniam" Date: Wed, 30 Dec 2009 01:16:28 -0500 Sent to CCL by: "Sangeetha Subramaniam" [srdshigella _ gmail.com] Hi, I would like to know the preliminary steps before calculating descriptors for a compound (other than protonation). I am using Dragon for descriptor calculation. Since Dragon doesn't recognize disconnected structure (compounds with more than one structure in same file), I had to remove the smaller fragment of the compound. I am afraid doing so, because I might lose the complete information of the compound. Can anyone please guide me through. Thanks Sangeetha. From owner-chemistry@ccl.net Wed Dec 30 13:59:01 2009 From: "jaleel uc jaleel.uc-x-gmail.com" To: CCL Subject: CCL: Data processing before descriptor calculation Message-Id: <-40979-091230125737-10690-jnlS4A+kGAABFwyLtFuLwg|*|server.ccl.net> X-Original-From: jaleel uc Content-Type: multipart/alternative; boundary=001636e0a6fb90fd50047bf57052 Date: Wed, 30 Dec 2009 22:56:32 +0530 MIME-Version: 1.0 Sent to CCL by: jaleel uc [jaleel.uc]~[gmail.com] --001636e0a6fb90fd50047bf57052 Content-Type: text/plain; charset=ISO-8859-1 use preadmet and look for the difference still problem exist please inform On 12/30/09, Sangeetha Subramaniam srdshigella]~[gmail.com < owner-chemistry:+:ccl.net> wrote: > > > Sent to CCL by: "Sangeetha Subramaniam" [srdshigella _ gmail.com] > Hi, > > I would like to know the preliminary steps before calculating descriptors > for a compound (other than protonation). I am using Dragon for descriptor > calculation. Since Dragon doesn't recognize disconnected structure > (compounds with more than one structure in same file), I had to remove the > smaller fragment of the compound. > I am afraid doing so, because I might lose the complete information of the > compound. Can anyone please guide me through. > > Thanks > Sangeetha.> > > -- Dr U.C.A.Jaleel. lecturer in cheminformatics Malabar christian college calicut --001636e0a6fb90fd50047bf57052 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
use preadmet and look for the difference
still problem exist=A0 please inform


=A0
On 12/30/09, Sangeetha Subramaniam srdshigella]~[gmail.com= <owner-chemistry:+:ccl= .net> wrote:

Sent to CCL by: "Sangee= tha=A0=A0Subramaniam" [srdshigella _ gmai= l.com]
Hi,

I would like to know the preliminary steps before calculating=A0= =A0descriptors for a compound (other than protonation). I am using Dragon f= or descriptor calculation. Since Dragon doesn't recognize disconnected = structure (compounds with more than one structure in same file), I had to r= emove the smaller fragment of the compound.
I am afraid doing so, because I might lose the complete information of the = compound. Can anyone please guide me through.

Thanks
Sangeetha.


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--
Dr U.C.A.Jaleel.
lecturer in = cheminformatics
Malabar christian college
calicut=20 --001636e0a6fb90fd50047bf57052-- From owner-chemistry@ccl.net Wed Dec 30 22:14:00 2009 From: "Sanghwa Han hansh,kangwon.ac.kr" To: CCL Subject: CCL: Planarity of an amide group Message-Id: <-40980-091230221147-27954-7jb4iJb3bU5U1Mj7msU9vw()server.ccl.net> X-Original-From: "Sanghwa Han" Date: Wed, 30 Dec 2009 22:11:42 -0500 Sent to CCL by: "Sanghwa Han" [hansh~~kangwon.ac.kr] Dear colleagues, In Biochemistry textbooks, an amide bond (NH-CO) in a peptide is explained to be planar. But when I optimize a capped amino acid (e.g. ACE-Amino Acid-NME) using HF/6-31G* for RESP charge derivation, the dihedral HN-CO often deviates from planarity by as much as 20 degrees. Do I need to constrain the HN-CO to 0 degrees to obtain an optimized structure that is used in a RESP charge derivation? Does anybody know if the amide group can be non-planar in experimentally determined structures? Thanks. Sanghwa Han