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 Mon Nov 09 2020 - 01:00:02 PST
