From chemistry-request@server.ccl.net Fri Jan  3 15:23:03 2003
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Date: Fri, 3 Jan 2003 14:15:21 -0500
From: Rick Venable <rvenable@gandalf.cber.nih.gov>
To: tluchko <tluchko@ualberta.ca>
cc: chemistry@ccl.net
Subject: Re: CCL:CHARMM: GTP and GDP parameters
In-Reply-To: <3E165239@webmail.ualberta.ca>
Message-ID: <Pine.SGI.4.21.0301031411560.3640-100000@gandalf.cber.nih.gov>
ReplyTo: Rick_Venable@nih.gov
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This is a simple editing bug, and should be fixed in the next parameter
release.  To correct the problem:

	in ATP or ADP change the following atom types

ATOM C2'  CN7     0.14  !
	to
ATOM C2'  CN7B    0.14  !

	and

ATOM C5'  CN8    -0.08
	to
ATOM C5'  CN8B   -0.08



On Thu, 2 Jan 2003, tluchko wrote:
> I am trying to come up with some parameters for GTP and GDP bound to
> tubulin for the CHARMM27 parameter set.  My hope is to use ATP and
> ADP as a starting point, however, I have run into two problems.  
> The first is that CHARMM does not seem to like the ATP/ADP
> parameters themselves.  I get errors such as
> 
>  <CODES>: No angle parameters for     5 ( ON6B CN7  CN8 )
>  <CODES>: A TOTAL OF    5 MISSING PARAMETERS
> 
>       ***** LEVEL -1 WARNING FROM <CODES> *****
>       ***** CODES> MISSING PARAMETERS
>       ******************************************
>       BOMLEV ( -2) IS NOT REACHED. WRNLEV IS  5
> 
>  CHECKDH> dihedral :    1   28   31   32 will NOT be generated
> 
> Is there something wrong with the parameters?  If these parameters are 
> supposed to be missing for ADP/ATP why is this correct?


=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=
Rick Venable           29/500
FDA/CBER/OVRR Biophysics Lab
1401 Rockville Pike    HFM-419
Rockville, MD  20852-1448  U.S.A.
(301) 496-1905   Rick_Venable@nih.gov
ALT email:  rvenable@speakeasy.org
=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=



From chemistry-request@server.ccl.net Fri Jan  3 14:41:11 2003
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From: "Tapas Kar" <tapaskar@cc.usu.edu>
To: "CCL" <chemistry@ccl.net>
Subject: Spectral info. of H3BNH3
Date: Fri, 3 Jan 2003 12:38:33 -0700
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Hi,
I am looking for IR/NMR (experiment) spectral information of H3BNH3
molecule.
Tapas

-----------------------------------------
Wish you all a very happy
and prosperous new year-2003
------------------------------------------
***********************************************
"We owe a lot to the Indians, who taught us how to count, without
which no worthwhile scientific discovery could have been made."
                                           - Albert Einstein -
----------------------------------------------------------------------------
----
Tapas Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax: 435-797-3390
Email: tapaskar@cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html


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<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
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class=3D064382119-03012003></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
class=3D064382119-03012003>Hi,</SPAN></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN =
class=3D064382119-03012003>I am=20
looking for IR/NMR (experiment) spectral information&nbsp;of H3BNH3 =
molecule.=20
</SPAN></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
class=3D064382119-03012003>Tapas</SPAN></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
class=3D064382119-03012003></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
class=3D064382119-03012003>-----------------------------------------</SPA=
N></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN =
class=3D064382119-03012003>Wish you=20
all a very happy&nbsp;</SPAN></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN =
class=3D064382119-03012003>and=20
prosperous new year-2003</SPAN></FONT></DIV>
<DIV><FONT face=3D"Comic Sans MS" size=3D2><SPAN=20
class=3D064382119-03012003>------------------------------------------</SP=
AN></FONT></DIV>
<P align=3Dleft><FONT=20
size=3D2>***********************************************<BR>"<FONT=20
face=3D"Comic Sans MS" size=3D1>We owe a lot to the Indians, who taught =
us how to=20
count, without<BR>which no worthwhile scientific discovery could have =
been=20
made."</FONT><BR>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&n=
bsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nb=
sp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbs=
p;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;=20
- Albert Einstein=20
-<BR>--------------------------------------------------------------------=
------------<BR>Tapas=20
Kar, Ph. D<BR>Department of Chemistry &amp; Biochemistry<BR>Utah State=20
University<BR>Logan, UT 84322-0300<BR><BR>Tel: 435-797-7230<BR>Fax:=20
435-797-3390<BR>Email: tapaskar@cc.usu.edu<BR><FONT face=3D"Comic Sans =
MS"=20
size=3D1>Web:</FONT><A=20
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size=3D1>http://www.chem.usu.edu/faculty/Tapas/index.html</FONT></A></FON=
T></P>
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From chemistry-request@server.ccl.net Fri Jan  3 23:50:30 2003
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Date: Sat, 4 Jan 2003 13:03:04 +0800 (HKT)
From: Ma Chi Chiu <martin@yangtze.hku.hk>
To: CHEMISTRY@ccl.net
Subject: Question
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Hi,

I have a question regarding using InsightII Charmm.
Actually, I am trying to optimize the sturcture (polymer) with periodic 
boundaries condition. However, I can't set it up correctly (the program 
always only consider the VDW between the primary atoms and image atoms). 

Then, I found the following sentences in the manual:
"A facility is also available to introduce bond linkages(with additional 
energy terms including angles, dihedrals, and improper dihedrals) between 
the primary and image atoms. This allows important polymers such as DNA 
or protein alpha helics to be studied." 

How to set up the bond linkages between primary atoms and image atoms? 

Thank you very much

Martin