From owner-chemistry@ccl.net Sat Oct 13 03:26:00 2012
From: "mina haghdadi mhaghdadi2 ~ yahoo.co.uk" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: hammet constant
Message-Id: <-47759-121013032135-26066-GIGYuCzkC9DeCGTO9S4Nrw ~ server.ccl.net>
X-Original-From: "mina  haghdadi" <mhaghdadi2- -yahoo.co.uk>
Date: Sat, 13 Oct 2012 03:21:33 -0400


Sent to CCL by: "mina  haghdadi" [mhaghdadi2[-]yahoo.co.uk]
Dear freinds,
I would like to calculate hmmet constants for some molecules which have substituents on aromatic rings, How can i calculate on B3LYP level. 
Best regards
Mona


From owner-chemistry@ccl.net Sat Oct 13 04:00:00 2012
From: "Shinaj Rajagopal K shinaj[-]iisertvm.ac.in" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: Maestro software
Message-Id: <-47760-121013013815-12882-ov8zyDGw+p7SJkV9dgawtA!^!server.ccl.net>
X-Original-From: "Shinaj Rajagopal K" <shinaj-#-iisertvm.ac.in>
Date: Sat, 13 Oct 2012 01:38:14 -0400


Sent to CCL by: "Shinaj Rajagopal K" [shinaj/a\iisertvm.ac.in]
I was trying to minimize the structure of a G-quadruplex structure which i 
downloaded from the PDB bank. But while i was running for the minimization 
using MacroModel with Schrodinger software Maestro 9.1, error generating 
interactions, aborted the minimization of the structure.
The crytal structure(PDB code: 1KF1)was downloaded as pdb file and was put in 
the Maestro software for getting the minimized structure.

Is the integrity of the structure lost while i download the file from data 
bank? If so can anyone suggest me how to download in a proper way from the PDB 
bank, since these structures are minimized and uploaded to the data bank.


From owner-chemistry@ccl.net Sat Oct 13 13:36:00 2012
From: "David Watson dewatson^^go.olemiss.edu" <owner-chemistry]|[server.ccl.net>
To: CCL
Subject: CCL: Maestro software
Message-Id: <-47761-121013103752-3077-cIJXanajna8XTEPZRTYTjQ]|[server.ccl.net>
X-Original-From: David Watson <dewatson|a|go.olemiss.edu>
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Date: Sat, 13 Oct 2012 09:37:41 -0500
Mime-Version: 1.0 (Mac OS X Mail 6.1 \(1498\))


Sent to CCL by: David Watson [dewatson_._go.olemiss.edu]
Many of the protein structures in the PDB are missing atoms, residues, etc.
In fact, you can bet that crystal structures (as opposed to NMR) for macromolecules will not have any hydrogens assigned.
If you are using Maestro, then you need to use the Protein Preparation Wizard to import the PDB file, generate atom types, add hydrogens, assign bond orders, etc.
One very important consideration before running any of the other Schrodinger utilities is to use the constrained minimization process in the Protein Preparation Wizard before using any of the other Schrodinger applications.

Best of luck

On Oct 13, 2012, at 12:38 AM, Shinaj Rajagopal K shinaj[-]iisertvm.ac.in <owner-chemistry,+,ccl.net> wrote:

> 
> Sent to CCL by: "Shinaj Rajagopal K" [shinaj/a\iisertvm.ac.in]
> I was trying to minimize the structure of a G-quadruplex structure which i 
> downloaded from the PDB bank. But while i was running for the minimization 
> using MacroModel with Schrodinger software Maestro 9.1, error generating 
> interactions, aborted the minimization of the structure.
> The crytal structure(PDB code: 1KF1)was downloaded as pdb file and was put in 
> the Maestro software for getting the minimized structure.
> 
> Is the integrity of the structure lost while i download the file from data 
> bank? If so can anyone suggest me how to download in a proper way from the PDB 
> bank, since these structures are minimized and uploaded to the data bank.
> 
> 
>


From owner-chemistry@ccl.net Sat Oct 13 23:16:01 2012
From: "Felipe Pineda pideca---hotmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL: Maestro software
Message-Id: <-47762-121013155126-26225-ivxrZrvIj0IcXD8xJkGTaw,+,server.ccl.net>
X-Original-From: Felipe Pineda <pideca__hotmail.com>
Content-Type: multipart/alternative;
	boundary="_518fefd3-fee4-40a4-a293-29fde9c55f32_"
Date: Sat, 13 Oct 2012 21:51:14 +0200
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Sent to CCL by: Felipe Pineda [pideca,+,hotmail.com]
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> From: owner-chemistry],[ccl.net
> To: fpineda],[uni-bonn.de
> Subject: CCL: Maestro software
> Date: Sat=2C 13 Oct 2012 09:37:41 -0500

> since these structures are minimized and uploaded to the data bank.

This is for sure not the case=2C except if your are calling "minimized" the=
 whole process of refining a difraction pattern=2C which undergo all protei=
n structures.=20
Kinda this is an example of the game of numbers indian science and financia=
l boom is all about. Take 1% or less of 10**9 people and you would have a l=
ot of people working in science without really having an eduactional founda=
tion for that.

Sorry for the politically incorrect remark=2C

Felipe

 		 	   		  =

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<html>
<head>
<style><!--
.hmmessage P
{
margin:0px=3B
padding:0px
}
body.hmmessage
{
font-size: 10pt=3B
font-family:Tahoma
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--></style></head>
<body class=3D'hmmessage'><div dir=3D'ltr'>
<br><div><div id=3D"SkyDrivePlaceholder"></div>&gt=3B From: owner-chemistry=
],[ccl.net<br>&gt=3B To: fpineda],[uni-bonn.de<br>&gt=3B Subject: CCL: Maestro =
software<br>&gt=3B Date: Sat=2C 13 Oct 2012 09:37:41 -0500<br><br><pre>&gt=
=3B since these structures are minimized and uploaded to the data bank.<br>=
<br>This is for sure not the case=2C except if your are calling "minimized"=
 the whole process of refining a difraction pattern=2C which undergo all pr=
otein structures. <br>Kinda this is an example of the game of numbers india=
n science and financial boom is all about. Take 1% or less of 10**9 people =
and you would have a lot of people working in science without really having=
 an eduactional foundation for that.<br><br>Sorry for the politically incor=
rect remark=2C<br><br>Felipe<br></pre><br></div> 		 	   		  </div></body>
</html>=

--_518fefd3-fee4-40a4-a293-29fde9c55f32_--


From owner-chemistry@ccl.net Sat Oct 13 23:50:00 2012
From: "Eric Bennett ericb],[pobox.com" <owner-chemistry###server.ccl.net>
To: CCL
Subject: CCL: Maestro software
Message-Id: <-47763-121013232547-4963-Uc3SV6Ky311L5FRce+lt5A###server.ccl.net>
X-Original-From: Eric Bennett <ericb(a)pobox.com>
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Date: Sat, 13 Oct 2012 23:25:34 -0400
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Sent to CCL by: Eric Bennett [ericb|a|pobox.com]

If the intention is to minimize it directly with Macromodel as Shinaj stated, then using some other minimization method beforehand could actually be counterproductive, although the other protein prep steps are still useful (for example it doesn't necessarily make sense to minimize with OPLS in protein prep if you are going to switch to some other force field in Macromodel).

This structure is a nucleic acid with potassium ions.  A couple possibly relevant points: (1) Not all of the force fields in Macromodel will have all of the parameters required for this system.  (2) The PDB file specifies bonds between oxygen atoms and the potassium ions.  Check to make sure the metal ions are free standing; the force fields generally do not accept metals that are input with explicit coordination bonds.

Cheers,
Eric



On Oct 13, 2012, at 10:37 AM, David Watson dewatson^^go.olemiss.edu wrote:

> 
> Sent to CCL by: David Watson [dewatson_._go.olemiss.edu]
> Many of the protein structures in the PDB are missing atoms, residues, etc.
> In fact, you can bet that crystal structures (as opposed to NMR) for macromolecules will not have any hydrogens assigned.
> If you are using Maestro, then you need to use the Protein Preparation Wizard to import the PDB file, generate atom types, add hydrogens, assign bond orders, etc.
> One very important consideration before running any of the other Schrodinger utilities is to use the constrained minimization process in the Protein Preparation Wizard before using any of the other Schrodinger applications.
> 
> Best of luck
> 
> On Oct 13, 2012, at 12:38 AM, Shinaj Rajagopal K shinaj[-]iisertvm.ac.in <owner-chemistry : ccl.net> wrote:
> 
>> 
>> Sent to CCL by: "Shinaj Rajagopal K" [shinaj/a\iisertvm.ac.in]
>> I was trying to minimize the structure of a G-quadruplex structure which i 
>> downloaded from the PDB bank. But while i was running for the minimization 
>> using MacroModel with Schrodinger software Maestro 9.1, error generating 
>> interactions, aborted the minimization of the structure.
>> The crytal structure(PDB code: 1KF1)was downloaded as pdb file and was put in 
>> the Maestro software for getting the minimized structure.
>> 
>> Is the integrity of the structure lost while i download the file from data 
>> bank? If so can anyone suggest me how to download in a proper way from the PDB 
>> bank, since these structures are minimized and uploaded to the data bank.
>> 
>> 
>> 
>