From owner-chemistry@ccl.net Tue Apr 14 03:07:00 2015 From: "Partha Sengupta anapspsmo[]gmail.com" To: CCL Subject: CCL: SLC6A4 solute carrier family 6 Message-Id: <-51255-150414020410-22370-yAZ15DO9HVRTaDJO3ylpfg#server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=089e013c614c727ca40513a8ffe4 Date: Tue, 14 Apr 2015 11:34:04 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo[#]gmail.com] --089e013c614c727ca40513a8ffe4 Content-Type: text/plain; charset=UTF-8 Friends, How can I get the structure of SLC6A4 solute carrier family 6 (neurotransmitter transporter), member 4 for molecular dynamics calculation? Partha -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --089e013c614c727ca40513a8ffe4 Content-Type: text/html; charset=UTF-8

Friends,

How can I get the structure of

SLC6A4 solute carrier family 6 (neurotransmitter transporter), member 4

for molecular dynamics calculation?

Partha

--

Dr. Partha Sarathi Sengupta
Associate Professor
Vivekananda Mahavidyalaya, Burdwan

--089e013c614c727ca40513a8ffe4-- From owner-chemistry@ccl.net Tue Apr 14 12:05:01 2015 From: "Safiya Amer amersaf85]=[yahoo.com" To: CCL Subject: CCL: Mixing Internal and Cartesian Coordinates Message-Id: <-51256-150414114545-32377-SPM4mjXR834iPft0VlhFHA . server.ccl.net> X-Original-From: Safiya Amer Content-Type: multipart/alternative; boundary="----=_Part_3130690_1683701705.1429026168779" Date: Tue, 14 Apr 2015 15:42:48 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: Safiya Amer [amersaf85() yahoo.com] ------=_Part_3130690_1683701705.1429026168779 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello all,Please, how can I construct mixed =C2=A0Cartesian and Internal Co= ordinates? Is there any way to construct it where variables in cartesian co= ordinates do not related with =C2=A0one in internal coordinates. I want to = do two things, First: optimization of a system H2-Fe(OH)3, second: calculat= ion of Molecular orbital coefficients to get wave function of the system.I = have this example but not well clear:****************It is also possible to= use both internal and Cartesian coordinates within the same Z-matrix, as i= n this example: O 0 xo =C2=A00. =C2=A0zoC 0 0. =C2=A0yc =C2=A00.C 0 0. -yc =C2=A00.N 0 xn = =C2=A00. =C2=A00.=C2=A0H 2 r1 3 a1 1 =C2=A0b1H 2 r2 3 a2 1 =C2=A0b2H 3 r1 2= a1 1 -b1H 3 r2 2 a2 1 -b2H 4 r3 2 a3 3 =C2=A0d3=C2=A0=C2=A0 Variables:=C2= =A0xo -1.zo =C2=A00.yc =C2=A01.xn =C2=A01.r1 1.08r2 1.08r3 1.02a1 125.a2 12= 5.d3 160.b1 =C2=A090.b2 -90.This Z-matrix has several features worth noting= : The variable names for the Cartesian coordinates are given symbolically in = the same manner as for internal coordinate variables. The integer 0 after the atomic symbol indicates symbolic Cartesian coordina= tes to follow. Cartesian coordinates can be related by a sign change just as dihedral angl= es can.*************************=C2=A0=C2=A0Finally, in this article ( =C2= =A0H. B. Schlegel, Int. J. Quant. Chem. Symp. 26, 243 (1992=C2=A0=C2=A0mixe= d internal and Cartesian coordinates were shown to have some advantages for= some cases. Regards for all Safiya AmerGraduate Studentamersaf85||yahoo.com=C2=A0h2feoh3||gmail.com=C2=A0 =C2=A0 ------=_Part_3130690_1683701705.1429026168779 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable

Hel= lo all,

Please, how can I construct mixed Cartesian and= Internal Coordinates? Is there any way to construct it where variables in = cartesian coordinates do not related with one in internal coordinates= . I want to do two things, First: optimization of a system H2-Fe(OH)3, seco= nd: calculation of Molecular orbital coefficients to get wave function of t= he system.

I have this example but not well clear:

****************

It is also possible to use both intern= al and Cartesian coordinates within the same Z-matrix, as in this example:<= /div>

O 0 xo 0. &nbs= p;zo

C 0 0. yc 0.

C 0 0. -yc = 0.

N 0 xn 0. 0.

H 2 r1 3 a1 1= b1

H 2 r2 3 a2 1 b2

H 3 r1 2 a1 1 = -b1

H 3 r2 2 a2 1 -b2

H 4 r3 2 a3 3 d3&nb= sp;

Variables:

xo -1.

zo 0.

yc 1.

xn 1.

r1 1.08

r2 1.08

r3 1.02

a1 = 125.

a2 125.

d3 160.

b1 90.=

b2 -90.

This Z-matrix has several features wor= th noting:

The varia= ble names for the Cartesian coordinates are given symbolically in the same = manner as for internal coordinate variables.

The integer 0 after the atomic symbol indicates sy= mbolic Cartesian coordinates to follow.

Cartesian coordinates can be related by a sign change = just as dihedral angles can.

*************************

<= div id=3D"yui_3_16_0_1_1429001094051_12177" style=3D"text-align: left;" cla= ss=3D"">

Finally, in this article ( H. B. S= chlegel, Int. J. Quant. Chem. Symp. 26, 243 (1992

= ;mixed internal and Cartesian coordinates were shown to have some advantage= s for some cases.

Regards for all

Safiya Amer

Graduate Student

amersaf85||yahoo.= com

= h2feoh3||gmail.com

=

------=_Part_3130690_1683701705.1429026168779-- From owner-chemistry@ccl.net Tue Apr 14 14:27:00 2015 From: "asmaa el-sayed asmaaphys88 . gmail.com" To: CCL Subject: CCL: calculate redox potential Message-Id: <-51257-150414133452-27965-fbfeIsi1HPKxeZQbe2227Q]=[server.ccl.net> X-Original-From: "asmaa el-sayed" Date: Tue, 14 Apr 2015 13:34:51 -0400 Sent to CCL by: "asmaa el-sayed" [asmaaphys88~!~gmail.com] Dear, all Does anyone know how to calculate the redox potential for compound in the ground state using gausssian? i need this redox potential to calculate the oxidation potential of the compound on the excited state.