Hi Dan,
Thank you for the clarification; that was really helpful.
Best,
Matthew
> On Mar 18, 2022, at 9:35 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> 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
