On 9/19/13 5:40 AM, xiao wrote:
Dear all,
I am developing the force field paramters of an organic molecule. I have a
trouble when i wrote the hydrogen atom database (.hdb) file. I do not know how
to write to control atom. The manual said that:
Three or four control atoms (i,j,k,l), where the first always is the atom to which the H
atoms are connected. The other two or three depend on the code selected. I can know the
meaning of the first control atom, but i am confused by "The other two or three
depend on the code selected". I think the other two control atoms are the heavy
atoms that are the neighbor of the heavy atom that is needed to add hydrogen. But how to
define the control atoms for the -CH3 group, because there is only one heavy atom that is
connected to the -CH3 group?
The control atoms are chosen based on the geometry of the group. Exact
specifications are given in manual section 5.6.4.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
==================================================
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