Quick follow up before I start, to cover all potential options one would have to throw in some wildcards right?
donormask :XXX./F*,O*,N*
To include OH and NX or similar in the analyses?
Best regards
// Gustaf
________________________________
Från: Gustaf Olsson <gustaf.olsson.lnu.se>
Skickat: den 23 november 2020 15:25:26
Till: AMBER Mailing List
Ämne: Re: [AMBER] cpptraj donor/acceptor definitions
No, not without trying to include the donor.
I will give that a try
Best regards
// Gustaf
On 23 Nov 2020, at 14:50, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
Hi,
On Mon, Nov 23, 2020 at 3:12 AM Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
This is actually what I ran, expecting hbond to behave as if not defining any donor/acceptor pairs.
donormask :XXX \
acceptormask :YYY \
Are you restricting it to F, O, and N atoms? E.g.
donormask :XXX./F,O,N
etc?
-Dan
This seems to have applied to any atoms meeting the criteria, detecting hydrogen bonds between C-H---H and other strange pairs.
When not supplying any masks at all the routine correctly identifies any donors/acceptors (that I have noticed so far at least). I wanted to be able to separate when a mask acts as a donor or acceptor with regard to lifetime (as I can sort ot donors/acceptors regarding occupancy with awk), this is when I noticed this somewhat peculiar behaviour.
I am using the most up to date amber20 version of cpptraj om mac right now.
Best regards
// Gustaf
On 20 Nov 2020, at 17:13, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
Hi,
Try omitting the donorhmask keyword. Hydrogens should then be picked
up automatically (make sure no hydrogens are selected by donormask).
-Dan
On Thu, Nov 19, 2020 at 5:46 AM Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
That’s what I figured. Hm, so is there a way to manipulate the use of wildcards to cover more instances, almost recreating not defining either donor/acceptor though just being able to specify what will be acting as a donor and what as an acceptor.
What I’m thinking of is defining something general like this:
donormask “:XXX & (.O= | .N= | .F=)" donorhmask “:XXX.H=" \
acceptormask “:YYY & (.O= | .N= | .F=)"
This does not work:
Error: There is not a 1 to 1 correspondance between donor and donorH masks.
For a test-system where XXX=YYY, the molecule is a carboxylic acid. I am trying to get any H which is attached to any O,N,F on any XXX molecule and check for hydrogen bonds with only O,N or F atoms. Trying the input above:
Error: donor (8 atoms), donorH (16 atoms).
So two oxygens per acid, 8 oxygens. This seems to be correct, however 16 H atoms is not. Only one of the oxygens has an acidic hydrogen, this should be 4. Even if the mask worked as intended, there would still not be a 1 to 1 correspondance (8:4).
Maybe there is no way of getting what I am looking for using wildcards and masks. I really just wanted to be able to separate bond information when molecules are acting as donors or acceptors as well as separate lifetime data for interactions without going through the hassle of defining every interacting pair manually.
Best regards
// Gustaf
On 18 Nov 2020, at 15:06, Daniel Roe <daniel.r.roe.gmail.com<mailto:daniel.r.roe.gmail.com>> wrote:
Hi,
The donormask/donorhmask/acceptormask keywords allow users to
fine-tune hydrogen bond selection; as stated in the manual, CPPTRAJ
will accept whatever you specify for these masks as hydrogen bond
donors and acceptors. To give users maximum flexibility, it does this
without double checking what the atoms are. So if you do something
like 'acceptormask *' then _every single atom_ is a potential hydrogen
bond donor. So you may just need to adjust your acceptormask to
exclude hydrogens (although I'm just guessing, not having seen your
input).
-Dan
On Wed, Nov 18, 2020 at 7:43 AM Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
Hello users and developers
While running hbond analysis without defining either donors/acceptors the “autodetect” function seemingly identifies pairs rather correctly (not including solvent). However, when running with defined donor/acceptor pairs though not defining donorhmask, there are a lot of instances where it seems that CPPTRAJ has identified a hydrogen forming a hydrogen bond with another hydrogen.
#Acceptor DonorH Donor Frames Frac AvgDist AvgAng
PHE_7.HE1 APM_12.H7 APM_12.C5 2 0.0002 2.9817 140.9910
I suppose that this is because these atoms fulfilled the criteria of a hydrogen bond with regard to angle and distance. However, unless I am misreading the output, this would indicate a
APM_12.C5 — APM_12.H7 ::: 1EH.7_PHE
Hydrogen bond being formed. For one, C5 would disqualify this as being a HBOND (no N/F/O) and the bond would be between H and H.
I suppose that this is not the correct way to use the definitions?
With a system including X, Y and WAT, what would be the input/masks required to run without defining any donor/acceptor information. Then running donor X vs acceptor Y and donor Y acceptor X?
Best regards
// Gustaf
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Received on Mon Nov 23 2020 - 07:00:02 PST
