From owner-chemistry@ccl.net Wed Aug 14 04:11:01 2013
From: "Prashant Kumar prashantkbio%gmail.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: protein ligand interaction analysis tool
Message-Id: <-49080-130814040853-13164-JgQ3z0Koi+41aPndmjrwpw!^!server.ccl.net>
X-Original-From: Prashant Kumar <prashantkbio/a\gmail.com>
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Date: Wed, 14 Aug 2013 10:08:26 +0200
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Sent to CCL by: Prashant Kumar [prashantkbio .. gmail.com]
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Dear Arnout Voet,

I would suggest you to use LIGPLOT. Here is the link to download the
program.
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/

Best,

Prashant


On Wed, Aug 14, 2013 at 4:43 AM, Arnout R.D. Voet arnout.voet++
fys.kuleuven.be <owner-chemistry*ccl.net> wrote:

>
> Sent to CCL by: "Arnout R.D. Voet" [arnout.voet ~ fys.kuleuven.be]
> Dear all,
> I am currently looking for a tool (preferably) working from the command
> line that investigates a protein ligand interaction and calculates some
> values liek the (total/polar/hydrophobic) contact surface area, number of
> hydrogens bonds ...
>
> is anyone aware of such a tool, or a package that can be used to do this
> kind of analysis.
>
> kindest regards
>
> Arnout Voet>
>
>

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<div dir=3D"ltr">Dear=A0<span style=3D"font-family:arial,sans-serif;font-si=
ze:13px">Arnout Voet,</span><div><span style=3D"font-family:arial,sans-seri=
f;font-size:13px"><br></span></div><div><font face=3D"arial, sans-serif">I =
would suggest you to use LIGPLOT. Here is the link to download the program.=
=A0</font></div>

<div><a href=3D"http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/">http:/=
/www.ebi.ac.uk/thornton-srv/software/LIGPLOT/</a><font face=3D"arial, sans-=
serif"><br></font></div><div><br></div><div>Best,</div><div><br></div><div>

Prashant</div></div><div class=3D"gmail_extra"><br><br><div class=3D"gmail_=
quote">On Wed, Aug 14, 2013 at 4:43 AM, Arnout R.D. Voet arnout.voet++<a hr=
ef=3D"http://fys.kuleuven.be">fys.kuleuven.be</a> <span dir=3D"ltr">&lt;<a =
href=3D"mailto:owner-chemistry*ccl.net" target=3D"_blank">owner-chemistry*c=
cl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><br>
Sent to CCL by: &quot;Arnout R.D. Voet&quot; [arnout.voet ~ <a href=3D"http=
://fys.kuleuven.be" target=3D"_blank">fys.kuleuven.be</a>]<br>
Dear all,<br>
I am currently looking for a tool (preferably) working from the command lin=
e that investigates a protein ligand interaction and calculates some values=
 liek the (total/polar/hydrophobic) contact surface area, number of hydroge=
ns bonds ...<br>


<br>
is anyone aware of such a tool, or a package that can be used to do this ki=
nd of analysis.<br>
<br>
kindest regards<br>
<br>
Arnout Voet<br>
<br>
<br>
<br>
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</blockquote></div><br></div>

--001a11c35760de444504e3e3dda7--


From owner-chemistry@ccl.net Wed Aug 14 07:30:00 2013
From: "Renier Dreyer renier.dreyer{}crunchyard.com" <owner-chemistry*server.ccl.net>
To: CCL
Subject: CCL: GROMACS Now on CrunchYard
Message-Id: <-49081-130814043549-23618-C7G1mouVDJFEnY6ldvvgjg*server.ccl.net>
X-Original-From: "Renier  Dreyer" <renier.dreyer{}crunchyard.com>
Date: Wed, 14 Aug 2013 04:35:47 -0400


Sent to CCL by: "Renier  Dreyer" [renier.dreyer(_)crunchyard.com]

CrunchYard is happy to announce that the versatile GROMACS package is now 
available for use on our system!

GROMACS simulates molecular dynamics with Newtonian equations of motion for 
systems with hundreds to millions of particles. Designed primarily for 
biochemical molecules like proteins, lipids and nucleic acids with complicated 
bonded interactions, but many chemists use it for research on non-biological 
systems, like polymers. This is because GROMACS is extremely fast at 
calculating non-bonded interactions as well.
 
Now you can get the speed of GROMACS for simulations, without the middle man, 
on a secure, global, 24/7, cost efficient, CrunchYard platform. Simply register 
at www.crunchyard.com or contact Dr Renier Dreyer at +27 (0) 11 717-6379 or 
renier.dreyer:+:crunchyard.com


From owner-chemistry@ccl.net Wed Aug 14 12:09:00 2013
From: "Vikram Seshadri vseshad!A!ncsu.edu" <owner-chemistry]~[server.ccl.net>
To: CCL
Subject: CCL: Regarding failure of DFT and working of MP2
Message-Id: <-49082-130814114125-2208-nalq3sTYQXYtGpebVF+Wog]~[server.ccl.net>
X-Original-From: "Vikram  Seshadri" <vseshad/./ncsu.edu>
Date: Wed, 14 Aug 2013 11:41:24 -0400


Sent to CCL by: "Vikram  Seshadri" [vseshad _ ncsu.edu]
Hi,

For one of my transition-state calculation, I found geometry optimization using MP2 method to work 
but DFT (B3LYP) failed. I was not sure why this was the case. I would greatly appreciate if someone 
count point to a reason for this with some references.

Thanks,

Vikram


From owner-chemistry@ccl.net Wed Aug 14 22:18:00 2013
From: "Joaquin Barroso Flores joaco_barroso*o*yahoo.com" <owner-chemistry|-|server.ccl.net>
To: CCL
Subject: CCL: Optimizing two fragments
Message-Id: <-49083-130814221632-9208-tq9E8RjQFuDz1GWFzuj/qA|-|server.ccl.net>
X-Original-From: Joaquin Barroso Flores <joaco_barroso],[yahoo.com>
Content-Type: multipart/alternative; boundary="-288413194-1593753438-1376532985=:35673"
Date: Wed, 14 Aug 2013 19:16:25 -0700 (PDT)
MIME-Version: 1.0


Sent to CCL by: Joaquin Barroso Flores [joaco_barroso-*-yahoo.com]
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Dear CCL comunity,=0A=0AIt's been a long time since I've posed a question i=
n this forum so I'm happy to reach out to the 'fresh faces' as well as the =
'timeless classics' of this community.=0A=0AI want to optimize two fragment=
s (simultaneously) in a host-guest compound but during the course of the ca=
lculation both fragments become too close and form bogus bonds (gaussview s=
hows a mess of them in those areas in close contact); the funny thing is th=
at some of them end up with normal terminations despite pentacoordinated Ca=
rbon atoms and such.=0AMy question is: Is there a way to perform this optim=
ization while forcing G09 to keep the connectivity matrix along the entire =
course of it?=A0=0Aboth host and guest are aromatic, thus the level of theo=
ry employed is B97D/lanl2dz (one of them includes an organometallic fragmen=
t).=0AStarting geometries: manually docked complex from isolated-optimized =
compounds.=0A=0AThanks in advanced for your help and your time. I will post=
 a summary with the answers you provide (that still exists, right?)=0A=0ABe=
st regards=0A=A0=0A=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=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=0AJoaquin Barroso-Flores, Ph. D.=0ACen=
tro Conjunto de Investigacion en Quimica Sustentable=0AInstituto de Quimica=
=0AUNAM=0A=0A=0A-> http://joaquinbarroso.wordpress.com=0A=0A=0Ajoaquin.barr=
oso''a''gmail.com =0A=0A=0A"Blogastronom=EDa": http://joaquinbarroso.blogsp=
ot.com =0A=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D
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<html><body><div style=3D"color:#000; background-color:#fff; font-family:ti=
mes new roman, new york, times, serif;font-size:14pt"><div><span>Dear CCL c=
omunity,</span></div><div style=3D"color: rgb(0, 0, 0); font-size: 19px; fo=
nt-family: 'times new roman', 'new york', times, serif; background-color: t=
ransparent; font-style: normal;"><span><br></span></div><div style=3D"color=
: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new york'=
, times, serif; background-color: transparent; font-style: normal;"><span>I=
t's been a long time since I've posed a question in this forum so I'm happy=
 to reach out to the 'fresh faces' as well as the 'timeless classics' of th=
is community.</span></div><div style=3D"color: rgb(0, 0, 0); font-size: 19p=
x; font-family: 'times new roman', 'new york', times, serif; background-col=
or: transparent; font-style: normal;"><span><br></span></div><div style=3D"=
color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman', 'new
 york', times, serif; background-color: transparent; font-style: normal;"><=
span>I want to optimize two fragments (simultaneously) in a host-guest comp=
ound but during the course of the calculation both fragments become too clo=
se and form bogus bonds (gaussview shows a mess of them in those areas in c=
lose contact); the funny thing is that some of them end up with normal term=
inations despite pentacoordinated Carbon atoms and such.</span></div><div s=
tyle=3D"color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new roman=
', 'new york', times, serif; background-color: transparent; font-style: nor=
mal;"><span>My question is: Is there a way to perform this optimization whi=
le forcing G09 to keep the connectivity matrix along the entire course of i=
t?&nbsp;</span></div><div style=3D"color: rgb(0, 0, 0); font-size: 19px; fo=
nt-family: 'times new roman', 'new york', times, serif; background-color: t=
ransparent; font-style: normal;"><span>both host and guest are aromatic,
 thus the level of theory employed is B97D/lanl2dz (one of them includes an=
 organometallic fragment).</span></div><div style=3D"color: rgb(0, 0, 0); f=
ont-size: 19px; font-family: 'times new roman', 'new york', times, serif; b=
ackground-color: transparent; font-style: normal;"><span>Starting geometrie=
s: manually docked complex from isolated-optimized compounds.</span></div><=
div style=3D"color: rgb(0, 0, 0); font-size: 19px; font-family: 'times new =
roman', 'new york', times, serif; background-color: transparent; font-style=
: normal;"><span><br></span></div><div style=3D"color: rgb(0, 0, 0); font-s=
ize: 19px; font-family: 'times new roman', 'new york', times, serif; backgr=
ound-color: transparent; font-style: normal;"><span>Thanks in advanced for =
your help and your time. I will post a summary with the answers you provide=
 (that still exists, right?)</span></div><div style=3D"color: rgb(0, 0, 0);=
 font-size: 19px; font-family: 'times new roman', 'new york', times, serif;
 background-color: transparent; font-style: normal;"><span><br></span></div=
><div style=3D"color: rgb(0, 0, 0); font-size: 19px; font-family: 'times ne=
w roman', 'new york', times, serif; background-color: transparent; font-sty=
le: normal;"><span>Best regards</span></div><div></div><div>&nbsp;</div><di=
v>=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D<br>Joaquin Barroso-Flores, Ph. D.<br>Centro Conjunto de =
Investigacion en Quimica Sustentable<br>Instituto de Quimica<br>UNAM</div><=
div><br><br></div><div> -&gt; http://joaquinbarroso.wordpress.com</div><br>=
<div><br></div><div>joaquin.barroso''a''gmail.com </div><div><br><br></div>=
<div>"Blogastronom=EDa": http://joaquinbarroso.blogspot.com <br>=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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D</div></div></body></html>
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