Added to my hbond to-do list that I really hope to get to one day...
https://github.com/Amber-MD/cpptraj/issues/392
On Mon, Nov 9, 2020 at 3:45 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
>
> Oh, one more thing which popped up, is there a keyword to include water in the analyses without needing to specify it as being a donor/acceptor (having it included with the “auto-detection” results).
>
> Best regards
> Gustaf
>
> > On 9 Nov 2020, at 09:40, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >
> > Setting the debug level > 1 did produce a promising start:
> >
> > HBOND: Searching for Hbond donors/acceptors in region specified by *
> > Distance cutoff = 3.000, Angle Cutoff = 135.000
> >
> > The printout from running the analysis with no additional input produces a list of "Acceptor-only atoms” and "Donor/acceptor sites”. This is roughly what I was looking for. I can solve this with some awk/grep combination though what I was hoping for was the same output on a “per resname” basis. My test system had 100 carboxylic acid molecules and water. I get 100 entries for the "carbonyl oxygen" and another 100 for the “hydroxyl group”. I was hoping to get entries on a “residue name/type” basis “on XXX found these acceptors/donors, on YYY, on ZZZ”.
> >
> > Don’t know if this is of any greater interest to anyone else and should most likely not be considered a priority issue.
> >
> > Thank you for you reply and suggestion
> > Best regards
> > // Gustaf
> >
> >
> >> On 6 Nov 2020, at 14:53, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >>
> >> Hi,
> >>
> >> On Fri, Nov 6, 2020 at 4:25 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >>> I was curious regarding the definition of hbond donors/acceptors in cpptraj. From what I understand, cpptraj allows a relatively loose definition of these and is capable of of some degree of auto-detection.
> >>
> >> As stated in the manual, a hydrogen bond in the hbond command is
> >> defined as being between an acceptor heavy atom A, a donor hydrogen
> >> atom H, and a donor heavy atom D. If the A to D distance is less than
> >> the distance cutoff (default 3 Ang) and the A-H-D angle is greater
> >> than the angle cutoff (default 135 deg.) a hydrogen bond is considered
> >> formed. Both cutoffs can be adjusted by the user.
> >>
> >>>
> >>> If my understanding is correct, is it possible to run cpptraj in a way, potentially just using the prmtop/inpcrd files, to print out all identified donors/acceptors?
> >>
> >> You can do this by setting the actions debug level to something
> >> greater than 1 (so put e.g. 'debug actions 1' before the 'hbond'
> >> command) and running on 1 frame. Maybe that should be a keyword
> >> option...
> >>
> >> -Dan
> >>
> >>>
> >>> Best regards
> >>> // Gustaf
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Received on Tue Nov 10 2020 - 06:30:03 PST
