AMBER Archive (2009)

Subject: Re: [AMBER] OE and CG types

From: Jio M (jiomm_at_yahoo.com)
Date: Tue Dec 29 2009 - 22:18:51 CST

Thanks Dr. Carlos S., Dr. Dean C., Jason S.

Thanks for solving confusion :-)

regards; HaPpY NeW yEaR to all

JIomm

>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.

>Happy holidays!

>Jason

>The atom names on the left correspond to the convention of Greek alphabet,

>with alpha being "next to" the highest priority functional group, the C=O,

>whose carbon is simply labeled C and whose oxygen is named O.

>Beta, "next to that"...etc.

CA = the C alpha carbon

CB= the C beta carbon

CG= the C gamma carbon

CD = the C delta carbon

OE= the O in the epsilon position

>etc...

>Do not confuse those with the atom types...

>BTW, you have GLN up there, not GLU...

>Good luck...

>Dean

--- On Mon, 12/28/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: [AMBER] OE and CG types
To: "AMBER Mailing List" <amber_at_ambermd.org>
Date: Monday, December 28, 2009, 5:42 PM

it's important to keep in mind that the parm files are not descriptions of
specific molecules or residues. ff99SB is not a "protein" parameter set.
They are simply force field parameter sets. They may have information about
many molecule types, certainly are not limited to just proteins. If you look
at a prep or lib file, it will only use a subset of parameters in the parm
file. Similarly, for some molecules the parm file may be incomplete and may
need to be supplemented with a frcmod file. Therefore, the presence of a
certain atom type does not imply that protein need to have examples of that
atom type. As Jason points out, ff99SB may also eb used for carbohydrates or
other molecules, not just proteins. It's the prep or lib file that is only
for proteins.

On Fri, Dec 25, 2009 at 7:32 AM, Jason Swails <jason.swails_at_gmail.com>wrote:

> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

      
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber