[gmx-users] specbonds

[Justin Lemkul]

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

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

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340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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