Hi,
On Thu, Mar 17, 2022 at 12:23 PM Matthew Guberman-Pfeffer
<matthew.guberman-pfeffer.uconn.edu> wrote:
> Why did the H-bond to GLN_1009.HB2 not appear in the output from the first command? Do the two commands use different criteria?
Yes; the commands are using the criteria you specified in each case.
This is outlined pretty clearly in the manual:
```
Potential hydrogen bond donor/acceptor atoms are searched for as follows:
1. If just <mask> is specified donors and acceptors will be
automatically determined from <mask>.
2. If donormask is specified donors will be determined from <dmask>
(only atoms bonded to hydrogen will be considered valid). Optionally,
donorhmask can be used in conjunction with donormask to explicitly
specify the hydrogen atoms bonded to donor atoms. Acceptors will be
automatically determined from <mask>.
3. If acceptormask is specified acceptors will be determined from
<amask>. Donors will be automatically determined from <mask>.
4. If both acceptormask and donormask are specified only <amask> and
<dmask> will be used; no searching will occur in <mask>.
Automatic determination of hydrogen bond donors/acceptors uses the
simplistic criterion that “hydrogen bonds are FON”, i.e., hydrogens
bonded to F, O, and N atoms are considered donors, and F, O, and N
atoms are considered acceptors.
```
So for your first command:
> hbond All out All.hbvtime.dat solventdonor :WAT solventacceptor :WAT.O \
> avgout All.UU.avg.dat solvout All.UV.avg.dat bridgeout All.bridge.avg.dat
Cpptraj is automatically determining donors/acceptors according to the
FON criterion. For your second command:
> hbond donormask :1018 acceptormask :X avgout temp_Res_1018-X_avg.dat
You are saying that *all atoms* in mask :1018 are a potential donor,
and *all atoms* in :X are potential acceptors. This is what is giving
you such improbable results as:
> GLN_1009.HB2 ALA_1018.HA ALA_1018.CA 10 0.0268 2.9364 140.2398
Cpptraj will take 'donormask' and 'acceptormask' at face value, so you
need to really restrict those masks to atoms you want to consider as
donors or acceptors. Try something like :1018./F,O,N to restrict to
elements F, O, and N, etc.
-Dan
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Received on Fri Mar 18 2022 - 07:00:02 PDT
