AMBER Archive (2009)

Subject: [AMBER] OE and CG types

From: Jio M (jiomm_at_yahoo.com)
Date: Thu Dec 24 2009 - 03:26:43 CST

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

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?

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

      
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