[gmx-users] specbonds

Justin Lemkul jalemkul at vt.edu
Thu Aug 23 14:05:40 CEST 2018

On 8/23/18 4:09 AM, Momin Ahmad wrote:
> Hi,
> i have two different residues and i want a bond defines between them. 
> I know i have to use the specbond.dat file but how do i implement the 
> additional potentials like stretching/angles/dihedrals? Is it enough 
> to just describe them in ffbonded.itp? Example: i have CH3 and NH as 
> different residues and want a bond between C and N. For the topology i 
> want also to define the parameters for the N-H bond, H-C-N/C-N-H angles.

Yes, all bonded parameters go in ffbonded.itp.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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