From owner-chemistry@ccl.net Sat Apr 16 10:52:00 2011
From: "Giovanni Finoto Caramori caramori(_)qmc.ufsc.br" <owner-chemistry,,server.ccl.net>
To: CCL
Subject: CCL: problem in EDA calculation
Message-Id: <-44389-110415171336-22117-4FMTU538Fn6zfcXyHph0OA,,server.ccl.net>
X-Original-From: Giovanni Finoto Caramori <caramori_._qmc.ufsc.br>
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Sent to CCL by: Giovanni Finoto Caramori [caramori||qmc.ufsc.br]
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Dear Kaul,

In your output check the SCF convergence. Probably it is unconverged. look f=
or a sentence like this:

SCF IS UNCONVERGED, TOO MANY ITERATIONS

If the SCF is unconverged the wave functions is not reliable!

regards,

Giovanni

Citando "indu kaul indu.kaul _ iiserpune.ac.in" <owner-chemistry _ ccl.net>:

>
> Sent to CCL by: "indu=A0 kaul" [indu.kaul,iiserpune.ac.in]
> Dear All,
>
> I have newly started using GAMESS for EDA analysis of certain dimers.
> 1)I dont know the representation of writing 6-311++g** basis,can=20
> somebody tell how to do it.??
> 2)I ran EDA for a dimer at b3lyp/aug-cc-pvdz and the result shows:
> ALL BASIS SET=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0HARTREE=A0 =A0 =A0 =A0 =A0 KCAL/MOL
>=A0 -------------
>=A0 ELECTROSTATIC ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ES=3D=A0 =A0 =
=A0 =A0 =A0-1.236592=A0 =A0 =A0 =A0 =A0=20
>=A0 -775.97
>=A0 EXCHANGE ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0EX=3D=A0 =
=A0 =A0 =A0 =A0-1.002818=A0 =A0 =A0 =A0 =A0=20
>=A0 -629.28
>=A0 REPULSION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0REP=3D=A0 =
=A0 =A0 =A0 =A0 5.291539=A0 =A0 =A0 =A0 =A0=20
>=A0 3320.49
>=A0 POLARIZATION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 POL=3D=A0 =A0 =
=A0 =A0 =A0-3.962384=A0 =A0 =A0 =A0 =A0=20
> -2486.44
>=A0 DFT DISPERSION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0DISP=3D=A0 =A0 =A0 =
=A0 =A0-0.095027=A0 =A0 =A0 =A0 =A0=20
>=A0 =A0-59.63
>=A0 TOTAL INTERACTION ENERGY HF OR DFT=A0 =A0 =A0E=3D=A0 =A0 =A0 =A0 =A0-1.=
005283=A0 =A0 =A0 =A0 =A0=20
>=A0 -630.83
>
> How can the electrostatic energy be so huge..!!
> AM i doing something wrong in giving input??..The input i gave is :-
>=A0 $CONTRL SCFTYP=3DRHF RUNTYP=3DEDA DFTTYP=3DB3LYP MAXIT=3D200
>=A0 =A0 =A0MULT=3D1 ISPHER=3D1 COORD=3DUNIQUE NOSYM=3D1 $END
>=A0 $SYSTEM TIMLIM=3D525600=A0 MWORDS=3D50 MEMDDI=3D500 $ENDI
>=A0 $BASIS GBASIS=3DACCD $END
>=A0 $SCF DIRSCF=3D.TRUE. CONV=3D1.0D-04=A0 $END
>=A0 $LMOEDA MATOM(1)=3D15,11 MCHARG(1)=3D0,0
>=A0 =A0 =A0 MMULT(1)=3D1,1 $END
>=A0 $DATA
>
> It will be a great pleasure if somebody can help me out of it.?
> Thanks In Advance.............
> Indu Kaul
>
>
>
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=A0=20

______________________________________
Giovanni Finoto Caramori PhD
Departamento de Quimica - CFM-UFSC
Campus Universitario Trindade - C.P. 476
88040-900 Florianopolis/SC
http://www.qmc.ufsc.br/~caramori
Phone: ++55(48)3721-6844/6845/6846
Fax: ++55(48)3721-6852 Ramal 239
Mobile: ++55(48)9926-8342

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Dear Kaul,<br />
<br />
In your output check the SCF convergence. Probably it is unconverged. look f=
or a sentence like this:<br />
<br />
SCF IS UNCONVERGED, TOO MANY ITERATIONS<br />
<br />
If the SCF is unconverged the wave functions is not reliable!<br />
<br />
regards,<br />
<br />
Giovanni<br />
<br />
Citando &quot;indu kaul indu.kaul _ iiserpune.ac.in&quot; &lt;owner-chemistr=
y _ ccl.net&gt;:<br />
<br />
&gt;<br />
&gt; Sent to CCL by: &quot;indu=A0 kaul&quot; [indu.kaul,iiserpune.ac.in]<br=
 />
&gt; Dear All,<br />
&gt;<br />
&gt; I have newly started using GAMESS for EDA analysis of certain dimers.<b=
r />
&gt; 1)I dont know the representation of writing 6-311++g** basis,can <br />
&gt; somebody tell how to do it.&#63;&#63;<br />
&gt; 2)I ran EDA for a dimer at b3lyp/aug-cc-pvdz and the result shows:<br /=
>
&gt; ALL BASIS SET=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =
=A0 =A0 =A0 =A0 =A0 =A0HARTREE=A0 =A0 =A0 =A0 =A0 KCAL/MOL<br />
&gt;=A0 -------------<br />
&gt;=A0 ELECTROSTATIC ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 ES=3D=A0 =A0=
 =A0 =A0 =A0-1.236592=A0 =A0 =A0 =A0 =A0 <br />
&gt;=A0 -775.97<br />
&gt;=A0 EXCHANGE ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0EX=3D=
=A0 =A0 =A0 =A0 =A0-1.002818=A0 =A0 =A0 =A0 =A0 <br />
&gt;=A0 -629.28<br />
&gt;=A0 REPULSION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0REP=3D=A0=
 =A0 =A0 =A0 =A0 5.291539=A0 =A0 =A0 =A0 =A0 <br />
&gt;=A0 3320.49<br />
&gt;=A0 POLARIZATION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 POL=3D=A0 =A0=
 =A0 =A0 =A0-3.962384=A0 =A0 =A0 =A0 =A0 <br />
&gt; -2486.44<br />
&gt;=A0 DFT DISPERSION ENERGY=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0DISP=3D=A0 =A0 =
=A0 =A0 =A0-0.095027=A0 =A0 =A0 =A0 =A0 <br />
&gt;=A0 =A0-59.63<br />
&gt;=A0 TOTAL INTERACTION ENERGY HF OR DFT=A0 =A0 =A0E=3D=A0 =A0 =A0 =A0 =A0=
-1.005283=A0 =A0 =A0 =A0 =A0 <br />
&gt;=A0 -630.83<br />
&gt;<br />
&gt; How can the electrostatic energy be so huge..!!<br />
&gt; AM i doing something wrong in giving input&#63;&#63;..The input i gave =
is :-<br />
&gt;=A0 $CONTRL SCFTYP=3DRHF RUNTYP=3DEDA DFTTYP=3DB3LYP MAXIT=3D200<br />
&gt;=A0 =A0 =A0MULT=3D1 ISPHER=3D1 COORD=3DUNIQUE NOSYM=3D1 $END<br />
&gt;=A0 $SYSTEM TIMLIM=3D525600=A0 MWORDS=3D50 MEMDDI=3D500 $ENDI<br />
&gt;=A0 $BASIS GBASIS=3DACCD $END<br />
&gt;=A0 $SCF DIRSCF=3D.TRUE. CONV=3D1.0D-04=A0 $END<br />
&gt;=A0 $LMOEDA MATOM(1)=3D15,11 MCHARG(1)=3D0,0<br />
&gt;=A0 =A0 =A0 MMULT(1)=3D1,1 $END<br />
&gt;=A0 $DATA<br />
&gt;<br />
&gt; It will be a great pleasure if somebody can help me out of it.&#63;<br =
/>
&gt; Thanks In Advance.............<br />
&gt; Indu Kaul<br />
&gt;<br />
&gt;<br />
&gt;<br />
&gt; -=3D This is automatically added to each message by the mailing script =
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&gt;<br />
&gt;<br />
&gt;<br />
<p>=A0</p>
<p class=3D"imp-signature"><!--begin_signature-->___________________________=
___________<br />
Giovanni Finoto Caramori PhD<br />
Departamento de Quimica - CFM-UFSC<br />
Campus Universitario Trindade - C.P. 476<br />
88040-900 Florianopolis/SC<br />
<a target=3D"_blank" href=3D"http://www.qmc.ufsc.br/~caramori">http://www.qm=
c.ufsc.br/~caramori</a><br />
Phone: ++55(48)3721-6844/6845/6846<br />
Fax: ++55(48)3721-6852 Ramal 239<br />
Mobile: ++55(48)9926-8342<!--end_signature--></p><br />
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From owner-chemistry@ccl.net Sat Apr 16 11:27:00 2011
From: "Jeff Hammond jeff.science\a/gmail.com" <owner-chemistry^server.ccl.net>
To: CCL
Subject: CCL: computational chemistry on accelerators session at SAAHPC 2011
Message-Id: <-44390-110416105835-31984-2wRwpJ7st8wW+FLlbl6Vtg^server.ccl.net>
X-Original-From: "Jeff  Hammond" <jeff.science---gmail.com>
Date: Sat, 16 Apr 2011 10:58:32 -0400


Sent to CCL by: "Jeff  Hammond" [jeff.science\a/gmail.com]
Members of CCL working with GPUs may be interested in submitting to the 
computational chemistry session of SAAHPC 2011.  Please note the paper submission 
deadline of May 6, 2011.

Regards,

Jeff Hammond
Argonne Leadership Computing Facility
jhammond%x%alcf.anl.gov
http://www.linkedin.com/in/jeffhammond

===================================================================

SAAHPC 2011 call for papers

The 2011 Symposium on Application Accelerators in High-Performance Computing will be 
held July 19-21, 2011, in Knoxville, Tennessee, bringing together developers of 
hybrid computing architectures and computing accelerators and experts involved with 
the development of applications on such systems to exchange ideas and discuss issues 
and emerging challenges.

Presentations from technology developers and the academic user community are invited 
on the following topics:

- novel accelerator processors, systems, and architectures
- integration of accelerators with high-performance computing systems
- programming models for accelerator-based computing
- languages and compilers for accelerator-based computing
- run-time environments, profiling and debugging tools for accelerator-based 
computing
- scientific and engineering applications that use application accelerators

In addition to the general session, submissions are invited for the following 
domain-specific topics:

- Computational chemistry on accelerators (Chair: Jeff Hammond, Argonne Leadership 
Computing Facility)
- Lattice QCD (Chair: Steven Gottlieb, Indiana University, Bloomington)
- Weather and climate modeling (Chair: John Michalakes, National Renewable Energy 
Laboratory)
- Bioinformatics (Chair: Jeremy Buhler, Washington University in St. Louis)

Visit the EasyChair conference submission system to submit either a short paper (up 
to 4 pages, for a poster presentation) or a long paper (up to 10 pages, for an oral 
presentation), by May 6, 2011. All submissions will be reviewed by the Technical 
Program Committee and the accepted submissions will be presented as either oral 
presentations or posters.  Papers presented at the symposium will be included in the 
proceedings published by Conference Publishing Services (pending approval).

Important dates:

Submissions due: May 6, 2011
Presentation acceptance notification: June 6, 2011
Final papers due: June 30, 2011


From owner-chemistry@ccl.net Sat Apr 16 12:02:00 2011
From: "Henry Martinez hmartine~~gmail.com" <owner-chemistry[A]server.ccl.net>
To: CCL
Subject: CCL:G: Do Calculation without nitrogen lone pair
Message-Id: <-44391-110416113332-18278-C85t6km/arj/+S/oavk9/g[A]server.ccl.net>
X-Original-From: "Henry  Martinez" <hmartine^gmail.com>
Date: Sat, 16 Apr 2011 11:33:29 -0400


Sent to CCL by: "Henry  Martinez" [hmartine=gmail.com]
Hi everyone, 
I do have access to Gaussian 03, and I would like to know if there is any way to perform a calculation "telling" the calculation to not "use" the nitrogen lone pair during the optimization. I want to do this in order to compare the ground state of a molecule, with and without the nitrogen Lone pair. Thanks a lot for the help.


From owner-chemistry@ccl.net Sat Apr 16 12:48:01 2011
From: "Esteban Gabriel Vega Hissi egvega/./gmail.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL:G: Do Calculation without nitrogen lone pair
Message-Id: <-44392-110416124610-19669-CZNnVtlkZD1Nqvt/rGGAqQ],[server.ccl.net>
X-Original-From: Esteban Gabriel Vega Hissi <egvega!=!gmail.com>
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Sent to CCL by: Esteban Gabriel Vega Hissi [egvega.:.gmail.com]
--90e6ba3fcdcbbc718e04a10be44a
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Hi,

Try NBO implemented in Gaussian. I haven't perform anything like this but
I've read it's possible.
http://www.chem.wisc.edu/~nbo5/TUT_DEL.HTM

Hope this help

--=20
Esteban Gabriel Vega Hissi
=C1rea de Qu=EDmica F=EDsica
Departamento de Qu=EDmica
Universidad Nacional de San Luis
Argentina

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<div>Hi,</div><div><br></div>Try NBO implemented in Gaussian. I haven&#39;t=
 perform anything like this but I&#39;ve read it&#39;s possible.<div><a hre=
f=3D"http://www.chem.wisc.edu/~nbo5/TUT_DEL.HTM">http://www.chem.wisc.edu/~=
nbo5/TUT_DEL.HTM</a><br>

<br><div>Hope this help</div><div><br></div><div>-- <br>Esteban Gabriel Veg=
a Hissi<br>=C1rea de Qu=EDmica F=EDsica<br>Departamento de Qu=EDmica<br>Uni=
versidad Nacional de San Luis<br>Argentina<br><br>
</div></div>

--90e6ba3fcdcbbc718e04a10be44a--


From owner-chemistry@ccl.net Sat Apr 16 13:31:00 2011
From: "Rajan Chaudhari rchaudhari-,-mail.usp.edu" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: Docking small molecules in the binding site of metalloproteins
Message-Id: <-44393-110416131027-14187-Kk3j8A9mNVWgouhxb/SUVg++server.ccl.net>
X-Original-From: Rajan Chaudhari <rchaudhari~!~mail.usp.edu>
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Sent to CCL by: Rajan Chaudhari [rchaudhari]-[mail.usp.edu]
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Hi Poonam=2C
Read the following article:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744578/
PLOP is free for academic use. Manual: http://www.jacobsonlab.org/plop_manu=
al/plop_manual.htm=20
Autodock:
http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=3DScienti=
fic%20Questions
How can I set up the protonation state of my histidine sidechains?Histidine=
s can be neutral or positively charged. When neutral=2C they can be protona=
ted at the delta (HD1) or epsilon (HE2) positions. How can I set these up?U=
sing ADT
There is a command in ADT to help you decide on the protonation of the Hist=
idines=2C but you have to load the commands before you can use it: go to "F=
ile > Load Module" and then scroll down=2C click on "repairCommands"=2C and=
 then click "Load Module" followed by "Dismiss". Now=2C go to "Edit > Hydro=
gens > Edit Histidine Hydrogens".

If there are any histidines in your molecule=2C a panel will open up listin=
g each histidine residue along with a row of radio buttons. You can use the=
se to choose whether each histidine should be neutral=2C HD1=3B neutral=2C =
HE2=3B or protonated.

Using Reduce/Molprobity
There is a very nice tool called Reduce (with a web-accessible front end ca=
lled Molprobity) that can be used for adding hydrogens and optimising the h=
ydrogen-bond network by flipping amido groups in Asn and Gln sidechains=2C =
and His imidazole rings by 180=BA. It can also be used for evaluating the q=
uality of your protein structure. See:

Word=2C et al. (1999) "Asparagine and glutamine: using hydrogen atom contac=
ts in the choice of sidechain amide orientation" J. Mol. Biol. 285=2C 1733-=
1745.
You need to study your receptor's active site as well as mechanism of actio=
n of binding ligand. you will get idea about protonation state of amino aci=
ds before the ligand interaction and after ligand interaction.

Hope this helps. Best Luck!
Regards=2CRajan



> From: owner-chemistry,ccl.net
To: rchaudhari,mail.usp.edu
Subject: CCL: Docking small molecules in the binding site of metalloprotein=
s
Date: Fri=2C 15 Apr 2011 16:08:01 -0600

Hello

I am trying to dock some small molecules with a metalloprotein having manga=
nese ions in its binding site.The binding site of my receptor protein
comprises mostly His=2CAsp=2Cand Glu residues and it is known that the pres=
ence of
metal ions can alter the hydration and protonation state of these amino aci=
d
residues in the binding site.Please suggest me as how should I optimize the
metal ion parameters and the protonation states of these amino acid residue=
s in
the binding site.I am using Surflex-Dock (Tripos Inc.) and Autodock for doc=
king studies.Also=2C please suggest me some relevant articles in this regar=
d.

Thank you
=20




Prija Ponnan=20
=20
Research Student
Department of Chemistry
University of Delhi
Delhi-110007=2C India
&
Canadian Commonwealth Scholarship Program Scholar
College of Pharmacy and Nutrition
University of Saskatchewan
Saskatoon=2CSKN5C9=2CCanada
=20
 		 	   		  =

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<html>
<head>
<style><!--
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body.hmmessage
{
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<body class=3D'hmmessage'>
<font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">Hi Poonam=2C</f=
ont><div style=3D"font-family: Tahoma=3B font-size: 10pt=3B "><br></div><di=
v style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Read the following a=
rticle:</div><div style=3D"font-family: Tahoma=3B font-size: 10pt=3B "><br>=
</div><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">http=
://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744578/</font></div><div><font cla=
ss=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></font></div><div><f=
ont class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">PLOP is free for =
academic use.&nbsp=3B</font></div><div><font class=3D"Apple-style-span" fac=
e=3D"Tahoma" size=3D"2">Manual: http://www.jacobsonlab.org/plop_manual/plop=
_manual.htm&nbsp=3B</font></div><div><font class=3D"Apple-style-span" face=
=3D"Tahoma" size=3D"2"><br></font></div><div><font class=3D"Apple-style-spa=
n" face=3D"Tahoma" size=3D"2">Autodock:</font></div><div><font class=3D"App=
le-style-span" face=3D"Tahoma" size=3D"2"><br></font></div><div><font class=
=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">http://autodock.scripps.ed=
u/faqs-help/faq/faqsection_view?section=3DScientific%20Questions</font></di=
v><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></fo=
nt></div><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><=
meta charset=3D"utf-8"><h3 style=3D"color: black=3B background-color: trans=
parent=3B font-family: 'Lucida Grande'=2C Verdana=2C Lucida=2C Helvetica=2C=
 Arial=2C sans-serif=3B margin-top: 0px=3B margin-right: 0px=3B margin-bott=
om: 0.25em=3B margin-left: 0px=3B border-bottom-width: initial=3B border-bo=
ttom-style: none=3B border-bottom-color: initial=3B border-collapse: collap=
se=3B ">How can I set up the protonation state of my histidine sidechains?<=
/h3><p class=3D"portletContent even" style=3D"margin-top: 0px=3B margin-rig=
ht: 0px=3B margin-bottom: 0.75em=3B margin-left: 0px=3B line-height: 1.5em=
=3B background-color: rgb(222=2C 236=2C 255)=3B border-collapse: collapse=
=3B font-family: 'Lucida Grande'=2C Verdana=2C Lucida=2C Helvetica=2C Arial=
=2C sans-serif=3B ">Histidines can be neutral or positively charged. When n=
eutral=2C they can be protonated at the delta (HD1) or epsilon (HE2) positi=
ons. How can I set these up?</p><div class=3D"portletContent odd" style=3D"=
background-color: transparent=3B padding-top: 1em=3B padding-right: 1em=3B =
padding-bottom: 1em=3B padding-left: 1em=3B border-collapse: collapse=3B fo=
nt-family: 'Lucida Grande'=2C Verdana=2C Lucida=2C Helvetica=2C Arial=2C sa=
ns-serif=3B "><p style=3D"margin-top: 0px=3B margin-right: 0px=3B margin-bo=
ttom: 0.75em=3B margin-left: 0px=3B line-height: 1.5em=3B "></p><h3 style=
=3D"color: black=3B background-color: transparent=3B font-family: 'Lucida G=
rande'=2C Verdana=2C Lucida=2C Helvetica=2C Arial=2C sans-serif=3B margin-t=
op: 0px=3B margin-right: 0px=3B margin-bottom: 0.25em=3B margin-left: 0px=
=3B border-bottom-width: initial=3B border-bottom-style: none=3B border-bot=
tom-color: initial=3B ">Using ADT</h3><br>There is a command in ADT to help=
 you decide on the protonation of the Histidines=2C but you have to load th=
e commands before you can use it: go to "File &gt=3B Load Module" and then =
scroll down=2C click on "repairCommands"=2C and then click "Load Module" fo=
llowed by "Dismiss". Now=2C go to "Edit &gt=3B Hydrogens &gt=3B Edit Histid=
ine Hydrogens".<br><br>If there are any histidines in your molecule=2C a pa=
nel will open up listing each histidine residue along with a row of radio b=
uttons. You can use these to choose whether each histidine should be neutra=
l=2C HD1=3B neutral=2C HE2=3B or protonated.<br><br><h3 style=3D"color: bla=
ck=3B background-color: transparent=3B font-family: 'Lucida Grande'=2C Verd=
ana=2C Lucida=2C Helvetica=2C Arial=2C sans-serif=3B margin-top: 0px=3B mar=
gin-right: 0px=3B margin-bottom: 0.25em=3B margin-left: 0px=3B border-botto=
m-width: initial=3B border-bottom-style: none=3B border-bottom-color: initi=
al=3B ">Using Reduce/Molprobity</h3><br>There is a very nice tool called&nb=
sp=3B<span class=3D"link-external" style=3D"background-image: initial=3B ba=
ckground-attachment: initial=3B background-origin: initial=3B background-cl=
ip: initial=3B background-color: transparent=3B padding-top: 0px=3B padding=
-right: 0px=3B padding-bottom: 0px=3B padding-left: 0px=3B background-posit=
ion: 0px 0px=3B background-repeat: no-repeat no-repeat=3B "><a href=3D"http=
://kinemage.biochem.duke.edu/software/reduce.php" style=3D"color: rgb(204=
=2C 102=2C 102)=3B background-color: transparent=3B ">Reduce</a></span>&nbs=
p=3B(with a web-accessible front end called&nbsp=3B<span class=3D"link-exte=
rnal" style=3D"background-image: initial=3B background-attachment: initial=
=3B background-origin: initial=3B background-clip: initial=3B background-co=
lor: transparent=3B padding-top: 0px=3B padding-right: 0px=3B padding-botto=
m: 0px=3B padding-left: 0px=3B background-position: 0px 0px=3B background-r=
epeat: no-repeat no-repeat=3B "><a href=3D"http://molprobity.biochem.duke.e=
du/" style=3D"color: rgb(204=2C 102=2C 102)=3B background-color: transparen=
t=3B ">Molprobity</a></span>) that can be used for adding hydrogens&nbsp=3B=
and&nbsp=3Boptimising the hydrogen-bond network by flipping amido groups in=
 Asn and Gln sidechains=2C and His imidazole rings by 180=BA. It can also b=
e used for evaluating the quality of your protein structure. See:<br><br>Wo=
rd=2C&nbsp=3B<span style=3D"font-style: italic=3B ">et al.</span>&nbsp=3B(1=
999) "Asparagine and glutamine: using hydrogen atom contacts in the choice =
of sidechain amide orientation"<span style=3D"font-style: italic=3B ">&nbsp=
=3BJ. Mol. Biol.</span>&nbsp=3B285=2C 1733-1745.</div></font></div><div><fo=
nt class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></font></div><=
div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">You need to=
 study your receptor's active site as well as mechanism of action of bindin=
g ligand. you will get idea about protonation state of amino acids before t=
he ligand interaction and after ligand interaction.</font></div><div><font =
class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></font></div><div=
><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></font></d=
iv><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">Hope th=
is helps.&nbsp=3B</font><span class=3D"Apple-style-span" style=3D"font-fami=
ly: Tahoma=3B font-size: 13px=3B ">Best Luck!</span></div><div><font class=
=3D"Apple-style-span" face=3D"Tahoma" size=3D"2"><br></font></div><div><fon=
t class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">Regards=2C</font></=
div><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">Rajan<=
/font></div><div><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2=
"><br></font></div><div><font class=3D"Apple-style-span" face=3D"Tahoma" si=
ze=3D"2"><br></font></div><div><font class=3D"Apple-style-span" face=3D"Tah=
oma" size=3D"2"><br></font><br><div id=3D"SkyDrivePlaceholder" style=3D"fon=
t-family: Tahoma=3B font-size: 10pt=3B "></div><hr id=3D"stopSpelling" styl=
e=3D"font-family: Tahoma=3B font-size: 10pt=3B "><font class=3D"Apple-style=
-span" face=3D"Tahoma" size=3D"2">From: owner-chemistry,ccl.net</font><br><=
font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">To: rchaudhari,m=
ail.usp.edu</font><br><font class=3D"Apple-style-span" face=3D"Tahoma" size=
=3D"2">Subject: CCL: Docking small molecules in the binding site of metallo=
proteins</font><br><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D=
"2">Date: Fri=2C 15 Apr 2011 16:08:01 -0600</font><br><br><font class=3D"Ap=
ple-style-span" face=3D"Tahoma" size=3D"2">Hello</font><br><br><font class=
=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">I am trying to dock some s=
mall molecules with a metalloprotein having manganese ions in its binding s=
ite.</font><span class=3D"ecxtext12" id=3D"ecxmsg_txt" style=3D"font-family=
: Tahoma=3B font-size: 10pt=3B ">The binding site of my receptor protein
comprises mostly His=2CAsp=2Cand Glu residues and it is known that the pres=
ence of
metal ions can alter the hydration and protonation state of these amino aci=
d
residues in the binding site.Please suggest me as how should I optimize the
metal ion parameters and the protonation states of these amino acid residue=
s in
the binding site.</span><font class=3D"Apple-style-span" face=3D"Tahoma" si=
ze=3D"2">I am using Surflex-Dock (Tripos Inc.) and Autodock for docking stu=
dies.Also=2C please suggest me some relevant articles in this regard.</font=
><br><br><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">Thank =
you</font><br><font class=3D"Apple-style-span" face=3D"Tahoma" size=3D"2">&=
nbsp=3B</font><br><br><br><br><br><br clear=3D"all"><font class=3D"Apple-st=
yle-span" face=3D"Tahoma" size=3D"2">Prija Ponnan=20
</font><div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">&nbsp=3B</=
div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Research Student<=
/div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Department of Che=
mistry</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">University of Del=
hi</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Delhi-110007=2C I=
ndia</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">&amp=3B</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Canadian Commonwe=
alth Scholarship Program Scholar</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">College of Pharma=
cy and Nutrition</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">University of Sas=
katchewan</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">Saskatoon=2CSKN5C=
9=2CCanada</div>
<div style=3D"font-family: Tahoma=3B font-size: 10pt=3B ">&nbsp=3B</div><br=
></div> 		 	   		  </body>
</html>=

--_a46d62f5-2e51-45b6-b4fd-911a42f696c1_--


From owner-chemistry@ccl.net Sat Apr 16 22:55:00 2011
From: "Hyunbok Lee mutebeat^-^gmail.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: treating unrestrict fragment on ADF
Message-Id: <-44394-110416224948-11661-9286R8MfinECTAe7UrbDWQ[]server.ccl.net>
X-Original-From: "Hyunbok  Lee" <mutebeat^gmail.com>
Date: Sat, 16 Apr 2011 22:49:38 -0400


Sent to CCL by: "Hyunbok  Lee" [mutebeat[-]gmail.com]
Dear all,

I'm trying to calculate transfer integrals between the identical molecules which have odd number electrons using ADF program.
However, I faced the error message "ERROR DETECTED: UNRESTRICTED FRAGMENT".

Can't unrestrict fragment be used on ADF?
If so, how can I solve this problem?

Thanks in advance.