AMBER Archive (2009)

Subject: Re: [AMBER] OE and CG types

From: Jason Swails (jason.swails_at_gmail.com)
Date: Fri Dec 25 2009 - 06:32:03 CST

On Fri, Dec 25, 2009 at 2:29 AM, Jio M <jiomm_at_yahoo.com> wrote:
> I was looking for CG on right column that is atom type CG in some amino acid. as it should be there in some amino acid. CG being sp2 as shown below in leap.ff99SB file
>
>
> /
> /{ "CE"  "C" "sp2" }
>    { "CF"  "C" "sp2" }
>    { "CG"  "C" "sp2" }
>

There are no such atom types in any of the amino acids used by ff99SB.
 The library of amino acids is
$AMBERHOME/dat/leap/lib/all_amino94.lib, and you will never see CG in
the second column. The atom TYPE CG is used in the GLYCAM force
fields which is used for, if I'm not mistaken, (poly)saccharides. The
CG name (not type) is used in all amino acids that have a Gamma carbon
(so all amino acids larger than glycine and alanine). Some of these
may be SP2 (such as ASP), whereas others will be SP3 (such as GLU and
LEU, etc.). However, the CG in glycam is type SP3, so I'm not quite
sure what this atom type is there for in ff99SB.

Another place you can look for these atom types is in the parm.dat
files in $AMBERHOME/dat/leap/parm. Look at parm94.dat, which is the
set of parameters used for proteins, and notice that there is also no
CG specified in it.

> thanks and regards;
> JIomm
>
>

Happy holidays!
Jason 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032

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