From owner-chemistry@ccl.net Tue Apr  6 05:46:01 2010
From: "allouche allouche#lasim.univ-lyon1.fr" <owner-chemistry||server.ccl.net>
To: CCL
Subject: CCL:G: Converting Gaussian .log NMR output to .jdx format
Message-Id: <-41604-100406034533-3357-PSdynCfptnDCkWeF/srY3A||server.ccl.net>
X-Original-From: allouche <allouche!^!lasim.univ-lyon1.fr>
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Date: Tue, 06 Apr 2010 08:59:14 +0200
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Sent to CCL by: allouche [allouche=lasim.univ-lyon1.fr]
Dear Robert,

Gabedit can simulate a NMR spectrum using the chemical shift and the 
spin-spin coupling
parameters calculated by Gaussian (or any other computation chemistry 
packages).

The simulated NMR spectrum can be compared to the experimental spectrum
(read from a jdx or a jMRUI file format).

After simulation, you can save the curve in a txt file (2 columns).

Gabedit is a free open source.
You can download it from : http://gabedit.sourceforge.net

Best regards,
A.R. Allouche

-- 
Abdul-Rahman ALLOUCHE
Fax : + (33) (0) 472431507
Email : allouche|-|lasim.univ-lyon1.fr
Web : http://sites.google.com/site/allouchear/



>Sent to CCL by: "Robert V. Kolakowski" [robertk-*-scripps.edu]
>Good Day,
>
>Has anyone out there found an off  the shelf solution for 
>converting Gaussian *.log NMR output to the universal
>*.jdx format?
>
>I'm trying to visualize calculated spin-spin couplings.
>
>Any help would be welcome.
>
>Cheers,
>
>Robert V.  Kolakowski, Ph.D.
>The Scripps Research Institute
>La Jolla, CA, 92037
>robertk],[scripps.edu
>
>  
>


From owner-chemistry@ccl.net Tue Apr  6 07:38:01 2010
From: "Kshatresh Dutta Dubey kshatresh*gmail.com" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: Negative NMODE
Message-Id: <-41605-100406073510-933-vwfZl1HNQJqJYsgQ95bsMA{=}server.ccl.net>
X-Original-From: Kshatresh Dutta Dubey <kshatresh|*|gmail.com>
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Date: Tue, 6 Apr 2010 17:05:04 +0530
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Sent to CCL by: Kshatresh Dutta Dubey [kshatresh++gmail.com]
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Dear All,
During the calculation of binding free energy i got negative entropic
contribution (NMODE= negative). Can entropic contributions be negative, and
what is the significance of it?
Every help is welcome. Thanks in advance.
Regards
kshatresh

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<div>Dear All,<br></div><div></div><div>During the calculation of binding free energy i got negative entropic contribution (NMODE= negative). Can entropic contributions be negative, and what is the significance of it?</div>
<div>Every help is welcome. Thanks in advance.</div><div></div><div>Regards</div><div>kshatresh</div>

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From owner-chemistry@ccl.net Tue Apr  6 11:52:01 2010
From: "Tatsiana Kirys nushki---mail.ru" <owner-chemistry~~server.ccl.net>
To: CCL
Subject: CCL: amino acid clashes
Message-Id: <-41606-100406105343-9522-kOzC4J0BcAaMiIYkXvMrLA~~server.ccl.net>
X-Original-From: "Tatsiana  Kirys" <nushki%%mail.ru>
Date: Tue, 6 Apr 2010 10:53:42 -0400


Sent to CCL by: "Tatsiana  Kirys" [nushki^^mail.ru]
Dear All,

i'm trying to figure out scheme for calculating protein amino acid clashes. I've read that

1) The overlap between two atoms is defined as the sum of their VDW radii minus the distance between them and minus an allowance for potentially hydrogen-bonded pairs:

    overlapij = rVDWi + rVDWj  dij  allowanceij

vdw_C = 1.70
vdw_N = 1.55
vdw_O = 1.52
vdw_P = 1.80
vdw_S = 1.80

allowanceij=0.4 (taken from "Penultimate rotamer library")
i calculated rotamer clashes from "Penultimate rotamer library" according to 1) for 1st D rotamer:
0 N ASP 1 -1.458 0.000 0.000
1 CA ASP 1 0.000 0.000 0.000
2 C ASP 1 0.551 -1.198 -0.766
3 CB ASP 1 0.536 0.000 1.433
4 CG ASP 1 0.292 1.315 2.147
5 OD1 ASP 1 -0.027 2.312 1.464
6 OD2 ASP 1 0.419 1.350 3.388 


i got the following clashes
 column 3 - first atom
 column 4 - second atom
 column 2 - vdw_radius_first_atom+vdw_radius_second_atom
 column 1 - distance between first and second atom

                        1        2    3 4

residue=1 has clash=2.461309 3.250000 0 2
residue=1 has clash=2.455509 3.250000 0 3
residue=1 has clash=3.066159 3.250000 0 4
residue=1 has clash=2.534580 3.400000 1 4
residue=1 has clash=2.736671 3.220000 1 5
residue=1 has clash=2.504202 3.400000 2 3
residue=1 has clash=2.379763 3.220000 3 5
residue=1 has clash=2.378700 3.220000 3 6
residue=1 has clash=1.249904 3.220000 4 5
residue=1 has clash=1.247972 3.220000 4 6
residue=1 has clash=2.196847 3.040000 5 6


i'm sure i do something wrong because "Penultimate rotamer library" was checked for the clashes.

could someone pleaseeeee help me with figuring out the correct procedure  

many thanks

Tania


From owner-chemistry@ccl.net Tue Apr  6 12:56:01 2010
From: "mattia mori.dott!^!gmail.com" <owner-chemistry__server.ccl.net>
To: CCL
Subject: CCL: Force Field parameters for Zinc and Chlorine
Message-Id: <-41607-100406105248-8438-3LXKy+swEPI/4NpqR8+LFQ__server.ccl.net>
X-Original-From: mattia <mori.dott|-|gmail.com>
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Date: Tue, 06 Apr 2010 16:21:54 +0200
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Sent to CCL by: mattia [mori.dott/a\gmail.com]
This is a multi-part message in MIME format.
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Hi Radek,
If you want to try with Zinc parameters developed for a similar system 
you could use these included in Mori M., et al, Journal of Chemical 
Information and Modeling, ASAP paper...
I developed a forcefield for a zinc-binding motif constituted by an 
histidine and three cysteines (one N and three S coordinating atoms).
Hope this help
regards

mattia

PS: in any case you could check the AMBER mailing list for more info...





Amir Taghavi amir_taghavi14a/yahoo.com ha scritto:
>
> Dear friend,
>
> you have to search the papers which regarding these specific 
> structures or any similarity to them. In fact you have to seek that if 
> any force field parameters have been developed for your aforementioned 
> atoms or not? You have to pay attention to their functional forms that 
> with what force field they match.
>
> Hope this is helpful.
>
> Regards,
>
> Amir
>
>
> --- On *Thu, 4/1/10, Radoslaw Kaminski rkaminski.rk**gmail.com 
> /<owner-chemistry*o*ccl.net>/* wrote:
>
>
>     From: Radoslaw Kaminski rkaminski.rk**gmail.com
>     <owner-chemistry*o*ccl.net>
>     Subject: CCL: Force Field parameters for Zinc and Chlorine
>     To: "Taghavi, Amir " <amir_taghavi14*o*yahoo.com>
>     Date: Thursday, April 1, 2010, 8:17 PM
>
>     Hi All,
>
>     Does anybody have an idea where I can found force field parameters
>     for Zn and Cl atoms? In my case the Zn atom is 4-coordinated to
>     two N atoms and two S atoms. The Cl atoms is bound to aromatic
>     phenyl ring. I was trying to use SYBYL/TRIPOS 5.2 or AMBER (as
>     implemented in ADF) but such atoms types are not included there.
>
>     Thanks for any help in advance.
>
>     All the best,
>
>     Radek
>
>


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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
  <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
  <title></title>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Radek,<br>
If you want to try with Zinc parameters developed for a similar system
you could use these included in Mori M., et al, Journal of Chemical
Information and Modeling, ASAP paper...<br>
I developed a forcefield for a zinc-binding motif constituted by an
histidine and three cysteines (one N and three S coordinating atoms). <br>
Hope this help<br>
regards<br>
<br>
mattia<br>
<br>
PS: in any case you could check the AMBER mailing list for more info...<br>
<br>
<br>
<br>
<br>
<br>
Amir Taghavi amir_taghavi14a/yahoo.com ha scritto:
<blockquote
 cite="mid:-id%233ur-41576-100402072836-14254-IGWnYIicdIUBLUY+548zzA\a/server.ccl.net"
 type="cite">
  <table border="0" cellpadding="0" cellspacing="0">
    <tbody>
      <tr>
        <td
 style="font-family: inherit; font-style: inherit; font-variant: inherit; font-weight: inherit; font-size: inherit; line-height: inherit; font-size-adjust: inherit; font-stretch: inherit;"
 valign="top">
        <div id="yiv1852270260">
        <p>Dear friend,</p>
        <p>you have to search the papers which regarding these specific
structures or any similarity to them. In fact you have to seek that if
any force field parameters have been developed for your aforementioned
atoms or not? You have to pay attention to their functional forms that
with what force field they match.<br>
        </p>
        <p>Hope this is helpful.</p>
        <p>Regards,</p>
        <p>Amir</p>
        <br>
--- On <b>Thu, 4/1/10, Radoslaw Kaminski rkaminski.rk**gmail.com <i>&lt;owner-chemistry*o*ccl.net&gt;</i></b>
wrote:<br>
        <blockquote
 style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>
> From: Radoslaw Kaminski rkaminski.rk**gmail.com
&lt;owner-chemistry*o*ccl.net&gt;<br>
Subject: CCL: Force Field parameters for Zinc and Chlorine<br>
To: "Taghavi, Amir " &lt;amir_taghavi14*o*yahoo.com&gt;<br>
Date: Thursday, April 1, 2010, 8:17 PM<br>
          <br>
          <div id="yiv570300447">Hi All,<br>
          <br>
Does anybody have an idea where I can found force field parameters for
Zn and Cl atoms? In my case the Zn atom is 4-coordinated to two N atoms
and two S atoms. The Cl atoms is bound to aromatic phenyl ring. I was
trying to use SYBYL/TRIPOS 5.2 or AMBER (as implemented in ADF) but
such atoms types are not included there.<br>
          <br>
Thanks for any help in advance.<br>
          <br>
All the best,<br>
          <br>
Radek<br>
          </div>
        </blockquote>
        </div>
        </td>
      </tr>
    </tbody>
  </table>
  <br>
</blockquote>
<br>
</body>
</html>

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From owner-chemistry@ccl.net Tue Apr  6 13:31:01 2010
From: "mattia mori.dott#%#gmail.com" <owner-chemistry%a%server.ccl.net>
To: CCL
Subject: CCL: Force Field parameters for Zinc and Chlorine
Message-Id: <-41608-100406113846-15693-yRp7TfZzFByC4eBm8ZEMIA%a%server.ccl.net>
X-Original-From: mattia <mori.dott*o*gmail.com>
Content-Transfer-Encoding: 7bit
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Date: Tue, 06 Apr 2010 17:38:41 +0200
MIME-Version: 1.0


Sent to CCL by: mattia [mori.dott:gmail.com]
Hi Radek,
If you want to try with Zinc parameters developed for a similar system 
you could use these included in Mori M., et al, Journal of Chemical 
Information and Modeling, ASAP paper...
I developed a forcefield for a zinc-binding motif constituted by an 
histidine and three cysteines (one N and three S coordinating atoms).
Hope this help
regards

mattia

PS: in any case you could check the AMBER mailing list for more info...



Amir Taghavi amir_taghavi14a/yahoo.com ha scritto:
>
> Dear friend,
>
> you have to search the papers which regarding these specific 
> structures or any similarity to them. In fact you have to seek that if 
> any force field parameters have been developed for your aforementioned 
> atoms or not? You have to pay attention to their functional forms that 
> with what force field they match.
>
> Hope this is helpful.
>
> Regards,
>
> Amir
>
>
> --- On *Thu, 4/1/10, Radoslaw Kaminski rkaminski.rk**gmail.com 
> /<owner-chemistry*o*ccl.net>/* wrote:
>
>
>     From: Radoslaw Kaminski rkaminski.rk**gmail.com
>     <owner-chemistry*o*ccl.net>
>     Subject: CCL: Force Field parameters for Zinc and Chlorine
>     To: "Taghavi, Amir " <amir_taghavi14*o*yahoo.com>
>     Date: Thursday, April 1, 2010, 8:17 PM
>
>     Hi All,
>
>     Does anybody have an idea where I can found force field parameters
>     for Zn and Cl atoms? In my case the Zn atom is 4-coordinated to
>     two N atoms and two S atoms. The Cl atoms is bound to aromatic
>     phenyl ring. I was trying to use SYBYL/TRIPOS 5.2 or AMBER (as
>     implemented in ADF) but such atoms types are not included there.
>
>     Thanks for any help in advance.
>
>     All the best,
>
>     Radek
>
>


From owner-chemistry@ccl.net Tue Apr  6 14:21:00 2010
From: "Elaine C Meng meng()cgl.ucsf.edu" <owner-chemistry!=!server.ccl.net>
To: CCL
Subject: CCL: amino acid clashes
Message-Id: <-41609-100406133303-2781-LtriY4+D5vnyEXHa/FnwCg!=!server.ccl.net>
X-Original-From: "Elaine C Meng" <meng-$-cgl.ucsf.edu>
Date: Tue, 6 Apr 2010 13:32:54 -0400


Sent to CCL by: "Elaine C Meng" [meng.]|[.cgl.ucsf.edu]
Tania's question was already answered on the chimera-users]|[cgl.ucsf.edu mailing list, see

http://www.cgl.ucsf.edu/pipermail/chimera-users/2010-April/005007.html

To summarize, she should be using the option in Chimera's
Find Clashes/Contacts tool to ignore pairs of atoms 
that are directly bonded or separated by only a few bonds.
That option is on by default.  The bonded atoms are often
closer together than would be expected from their VDW radii
alone, and if that option is turned off, those pairs will often
be identified as clashing even though they are not really clashes.

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco


From owner-chemistry@ccl.net Tue Apr  6 15:57:00 2010
From: "Roy Green powergreen _ gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL: Molpro
Message-Id: <-41610-100406154859-29749-snGXj9de6k8Czg9jGobWTw,server.ccl.net>
X-Original-From: Roy Green <powergreen]^[gmail.com>
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Date: Tue, 6 Apr 2010 15:48:32 -0400
MIME-Version: 1.0


Sent to CCL by: Roy Green [powergreen!=!gmail.com]
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Hi
Does anyone have experience of Molrpo calculations on GridChem? My jobs
sometimes stopped abnormally with job status showing "Time Elapsed", but
sometimes, the same jobs can finish normally. I will be very appreciated
with your advices.

Best regard

Roy

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Hi<br>Does anyone have experience of Molrpo calculations on GridChem? My jo=
bs sometimes stopped abnormally with job status showing &quot;Time Elapsed&=
quot;, but sometimes, the same jobs can finish normally. I will be very app=
reciated with your advices. <br>
<br>Best regard<br><br>Roy <br>

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