AMBER Archive (2009)

Subject: Re: [AMBER] OE and CG types

From: Jio M (jiomm_at_yahoo.com)
Date: Thu Dec 24 2009 - 09:18:31 CST

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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