AMBER Archive (2009)

Subject: Re: [AMBER] OE and CG types

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Dec 25 2009 - 01:29:19 CST

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" }

thanks and regards;
JIomm

________________________________
F/rom: Carlos Simmerling <carlos.simmerling_at_gmail.com>
To/: AMBER Mailing List <amber_at_ambermd.org>
Sen/t: Thu, December 24, 2009 9:08:24 PM
Subject: Re: [AMBER] OE and CG types

I think you're still confused - there is no CG atom type in Glu, it's an
atom named CG. names and atom types are different.
here are the GLU names (column 1) and atom types (column 2) for each atom -
this is from dat/leap/prep/all_amino94.in in case you want to know more.

N N
H H
CA CT
HA H1
CB CT
HB2 HC
HB3 HC
CG CT
HG2 HC
HG3 HC
CD C
OE1 O
NE2 N
HE21 H
HE22 H
C C
O O

On Thu, Dec 24, 2009 at 10:18 AM, Jio M <jiomm_at_yahoo.com> wrote:

> thanks for reply and solving my confusion. but still CG atom type couldnt
> find in amino acid :-) in lib file
>
>
>
>
> ________________________________
> From: Jason Swails <jason.swails_at_gmail.com>
> To: AMBER Mailing List <amber_at_ambermd.org>
> Sent: Thu, December 24, 2009 6:16:35 PM
> Subject: Re: [AMBER] OE and CG types
>
> Hello,
>
> This is fairly straightforward, but is very easy to confuse as well.
>
> On Thu, Dec 24, 2009 at 4:26 AM, Jio M <jiomm_at_yahoo.com> wrote:
> > Dear Amber users;
> >
> >
> >
> > May be this is very simple question.
> >
> > I have a protein having GLU residue has "OE" and "CG" (hydrogen removed)
> >
> > N GLU
> >
> > CA GLU
> >
> > C GLU
> >
> > O GLU
> >
> > CB GLU
> >
> > CG GLU
> >
> > CD GLU
> >
> > OE1 GLU
> >
> > OE2 GLU
> >
>
> These are not atom types. These are atom names, and as such act
> simply as labels for Leap. Each of these atom names have associated
> with them an atom type, and it's the atom type that is given
> characteristics (i.e. SP2, SP3, etc.). You can find the atom types
> corresponding to these atom names in the OFF library file associated
> with ff99SB (namely, all_amino94.lib in $AMBERHOME/dat/leap/lib/). CG
> has type CT, which is the same atom type as CA (and as such is SP3).
> CD is type C, and is SP2. Atoms OE1 and OE2 are (and should be) the
> same, but they need different names to distinguish them. Thus, they
> are both type O2, which you should be able to find attributes for.
>
>
> >
> >
> > when we source leaprc.ff99SB it uses parm99.dat and frcmod file. I am
> > not able to get that from where amber could recognise "OE" (other
> > examples may also be there).
> >
> >
> >
> > 1) "CG "I can see in "addAtomTypes" is sp2 but I was not able to find
> "OE" anywhere and what type of carbon CG is?
> >
>
> If this CG is really an atom type, then this is merely a coincidence
> and has nothing to do with the CG defined in your GLU residue.
>
>
> >
> >
> > 2) "CG" is written sp2 in leaprc.ff99SB file, but in xleap if "edit GLU"
> and see CG, it is sp3 carbon.
> >
> >
> >
> > please help to understand this confusion.
> >
> >
> >
> > thanks and regards; hApPy HoLiDaYs
> >
> > JIomm
> >
> >
>
> I hope this helps to clarify some of your confusing.
>
> Good luck, and happy holidays to all!
> Jason
>
> --
> ---------------------------------------
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
>
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>
>
>
>
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