[gmx-users] control atom in .hdb file

Justin Lemkul jalemkul at vt.edu
Thu Sep 19 13:53:44 CEST 2013

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 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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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