[gmx-users] h_bond

[Justin Lemkul]

On 6/15/16 3:23 AM, Shahid Nayeem wrote:
> Dear all
>
> I want to get number of hydrogen bonds between solvent(water) and alpha
> helix or beta sheet along the trajectory. Secondary structure of protein
> changes along the trajectory. Is it possible for gromacs to first find the
> secondary structure of snapshot and then calculate hydrogen bonds between
> SOL and each of the the secondary structure and then same for the next
> snapshots.
>

Calculate both quantities separately (gmx do_dssp and gmx hbond) then 
post-process the output files to parse the frames in which whatever criteria you 
like are satisfied.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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