AMBER: gaff "ha" atom type

From: Oliver Hucke <ohucke.u.washington.edu>
Date: Wed, 21 Apr 2004 13:38:20 -0700

Dear All,

I am using antechamber as part of amber8 for the preparation of a
protein ligand for my simulations.

Antechamber assigns the type "ha" to a hydrogen at an aliphatic sp2
carbon (type "c2"), which is connected only to other carbons.
Is the type "ha" correct for such a hydrogen?

 From the manuscript on the gaff force field I would expect such a
hydrogen to have the type "hc"?

Thanks very much,

Oliver 

-- 
_______________________________________________________________
Oliver Hucke, Dr.
                               Health Sciences Building - K418C
University of Washington      1959 NE Pacific St.
Dept. of Biochemistry         phone: (206) 685 7046
Box 357742                    fax  : (206) 685 7002
Seattle, WA 98195-7742        email: ohucke.u.washington.edu
_______________________________________________________________
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Apr 21 2004 - 21:53:00 PDT
Custom Search