From owner-chemistry@ccl.net Sat Sep 5 10:12:00 2009 From: "Cintia C. Vequi-Suplicy cintiadevequi+*+gmail.com" To: CCL Subject: CCL: Transition state calculation Message-Id: <-40173-090905082105-3034-zFSMSXi5lueLT8kpUE89Cw_._server.ccl.net> X-Original-From: "Cintia C. Vequi-Suplicy" Content-Type: multipart/alternative; boundary=0016e65b3ffc2210770472d2cbde Date: Sat, 5 Sep 2009 08:19:43 -0300 MIME-Version: 1.0 Sent to CCL by: "Cintia C. Vequi-Suplicy" [cintiadevequi%x%gmail.com] --0016e65b3ffc2210770472d2cbde Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hello, when I tried to do a ts optimization I used the following keywords and it worked and this error was gone: OPT=3D(TS,MaxCycles=3D500,CalcFC,NoEigenTest) SCF=3D(MaxCycles =3D1000) Fre= q But ts optimization are very delicate and something the result is not the desired ts state, in my case it wasn't. Greeting, --=20 C=EDntia C. Vequi Suplicy Grupo de Biof=EDsica Instituto de F=EDsica - USP - Brazil --0016e65b3ffc2210770472d2cbde Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable hello,

when I tried to do a ts optimization I used the following key= words and it worked and this error was gone:

OPT=3D(TS,MaxCycles=3D5= 00,CalcFC,NoEigenTest) SCF=3D(MaxCycles =3D1000) Freq

But ts optimiz= ation are very delicate and something the result is not the desired ts stat= e, in my case it wasn't.

Greeting,

--
C=EDntia C. Vequi Suplicy
Grupo de Biof=EDsi= ca
Instituto de F=EDsica - USP - Brazil

--0016e65b3ffc2210770472d2cbde-- From owner-chemistry@ccl.net Sat Sep 5 10:46:00 2009 From: "Green Power powergreen]^[gmail.com" To: CCL Subject: CCL:G: Current density map Message-Id: <-40174-090905022019-4767-UZ1Z/jtBPM1r/gwErsUHWQ###server.ccl.net> X-Original-From: Green Power Content-Type: multipart/alternative; boundary=00c09f97200849e4930472cd95f6 Date: Sat, 5 Sep 2009 01:06:45 -0400 MIME-Version: 1.0 Sent to CCL by: Green Power [powergreen|a|gmail.com] --00c09f97200849e4930472cd95f6 Content-Type: text/plain; charset=ISO-8859-1 Hi, All Anybody know how to visualize the current density map generalized by Gaussian cube file? In a previous message on the CCL, it is said CCP1GUI can do that. But there is little documentation for this package and I could not figure how to to do that. Could you give me any instructions if you have any experience about that. Thank you in advance. Tian --00c09f97200849e4930472cd95f6 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, All

Anybody know how to visualize the current density map genera= lized by Gaussian cube file? In a previous message on the CCL, it is said C= CP1GUI can do that. But there is little documentation for this package and = I could not figure how to to do that. Could you give me any instructions if= you have any experience about that. Thank you in advance.

Tian
--00c09f97200849e4930472cd95f6-- From owner-chemistry@ccl.net Sat Sep 5 12:16:01 2009 From: "Yingbin Ge yingbin.ge .. gmail.com" To: CCL Subject: CCL: molecular structure mapping Message-Id: <-40175-090905000350-10943-ey6VUXEDFuv++f3z4s6diQ^^server.ccl.net> X-Original-From: Yingbin Ge Content-Type: multipart/alternative; boundary=0016e6476dfe1c82900472c9e933 Date: Fri, 4 Sep 2009 17:43:51 -0700 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge(!)gmail.com] --0016e6476dfe1c82900472c9e933 Content-Type: text/plain; charset=ISO-8859-1 Hi, I wonder if there's a software that can deal with molecular structure mapping. For example, the following two structures are nearly identical but with different order. Does any code to do this kind of mapping automatically? C 0.0 0.0 0.0 H 0.0 0.0 1.0 H 0.0 0.0 -1.0 H 0.0 0.0 0.0 C 1.1 0.0 0.0 H 2.0 0.0 0.0 Thanks, Yingbin --0016e6476dfe1c82900472c9e933 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
=A0
I wonder if there's a software that can deal with=A0molecular stru= cture=A0mapping.
=A0
For example, the following two structures are nearly identical but wit= h different order.
Does any code to do this kind of mapping automatically?
=A0
C 0.0 0.0 0.0
H 0.0 0.0 1.0
H 0.0 0.0 -1.0
=A0
H 0.0 0.0 0.0
C 1.1 0.0 0.0
H 2.0 0.0 0.0
=A0
Thanks,
Yingbin

=A0
--0016e6476dfe1c82900472c9e933-- From owner-chemistry@ccl.net Sat Sep 5 16:06:01 2009 From: "Michel Petitjean petitjean.chiral[*]gmail.com" To: CCL Subject: CCL: molecular structure mapping Message-Id: <-40176-090905155635-18765-Xw92UGia7mZ4AtJGa7vVuA() server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 5 Sep 2009 21:33:50 +0200 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral:gmail.com] Try the freeware CSR: http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#CSR Michel Petitjean, DSV/iBiTec-S/SB2SM (CNRS URA 2096), CEA Saclay, bat. 528, 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean|a|cea.fr, petitjean.chiral|a|gmail.com http://petitjeanmichel.free.fr/itoweb.petitjean.html ---------- Forwarded message ---------- > From: Yingbin Ge yingbin.ge .. gmail.com Date: 2009/9/5 Subject: CCL: molecular structure mapping To: "Petitjean, Michel " Hi, I wonder if there's a software that can deal with molecular structure mapping. For example, the following two structures are nearly identical but with different order. Does any code to do this kind of mapping automatically? C 0.0 0.0 0.0 H 0.0 0.0 1.0 H 0.0 0.0 -1.0 H 0.0 0.0 0.0 C 1.1 0.0 0.0 H 2.0 0.0 0.0 Thanks, Yingbin From owner-chemistry@ccl.net Sat Sep 5 16:40:01 2009 From: "Ron Salesky rsalesky(a)unm.edu" To: CCL Subject: CCL: VMD SWCNT .psf generation question [resent by admin] Message-Id: <-40177-090904171304-23473-qtvxz6NhjgYP9NgDGFxIgQ]![server.ccl.net> X-Original-From: "Ron Salesky" Date: Fri, 4 Sep 2009 17:13:00 -0400 Sent to CCL by: "Ron Salesky" [rsalesky[A]unm.edu] [This message is being resent by Jan Labanowski -- I had some space problems in the /var partition, and this message may have been only partially distributed ] Hello, I've generated a SWCNT .pdb coordinate file using the VMD nanotube generator plug-in. Auto generating the .psf file runs into problems because the residue name in the .pdb file is "CNT". Does anyone have a recommendation for a residue name that is appropriate for a C bonded as a SWCNT (rolled up graphene) configuration? Thanks! Ron From owner-chemistry@ccl.net Sat Sep 5 18:00:00 2009 From: "Basma Ghazal basmaghazal!A!ymail.com" To: CCL Subject: CCL: Steps of docking Message-Id: <-40178-090905175855-15653-9ah6FTAGxNhUASNuchiZYQ#server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-401971660-1252187918=:57780" Date: Sat, 5 Sep 2009 14:58:38 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal : ymail.com] --0-401971660-1252187918=:57780 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Thanks for the first result but I read that I have to=A0add hydrogen then, = remove the polar one could you explain that please. --- On Sun, 8/30/09, Kalju Kahn kalju() chem.ucsb.edu wrote: > From: Kalju Kahn kalju() chem.ucsb.edu Subject: CCL: Steps of docking To: "Ghazal, Basma " Date: Sunday, August 30, 2009, 8:26 PM Sent to CCL by: "Kalju Kahn" [kalju]=3D[chem.ucsb.edu] Basma, One reason would be that the experimental structure was crystallized with a small ligand in a larger pocket, and the voids of that pocket contain water molecules.=A0 But you may want these voids be accessible to ligand atoms while docking.=A0 With standard docking methods, the water will not b= e "squeezed" out during binding, as would happen with real molecules, so you need to remove them.=A0 Of course, other times you may want to keep some of these waters in order to benefit from solvent-mediated interactions. Kalju > Hi: > Thanks for this result but I need to ask about somthing; > Why we remove water? > Thanks ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A --0-401971660-1252187918=:57780 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
Thanks for the first result but I read that = I have to add hydrogen then, remove the polar one could you explain th= at please.


--- On Sun, 8/30/09, Kalju Kahn kalju() chem.ucsb.edu &l= t;owner-chemistry**ccl.net> wrote:

From: Kalju Kahn kalju() chem.ucsb.edu <owner-= chemistry**ccl.net>
Subject: CCL: Steps of docking
To: "Ghazal, Bas= ma " <basmaghazal**ymail.com>
Date: Sunday, August 30, 2009= , 8:26 PM


Sent to CCL by: "Kalju Kahn" [kalju]=3D[chem.ucs= b.edu]
Basma,

One reason would be that the experimental structure= was crystallized with
a small ligand in a larger pocket, and the voids = of that pocket contain
water molecules.  But you may want these voi= ds be accessible to ligand
atoms while docking.  With standard dock= ing methods, the water will not be
"squeezed" out during binding, as wou= ld happen with real molecules, so you
need to remove them.  Of cour= se, other times you may want to keep some of
these waters in order to be= nefit from solvent-mediated interactions.

Kalju


> Hi:<= BR>> Thanks for this result but I need to ask about somthing;
> Wh= y we remove water?
> Thanks


~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~= ~~~
Dr. Kalju Kahn
Department of Chemistry and Biochemistry
UC San= ta Barbara, CA 93106



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