[gmx-users] control atom in .hdb file

xiao helitrope at 126.com
Thu Sep 19 11:40:45 CEST 2013

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?

Any suggestion is appreciated.

Best wishes


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