Hi,
On Mon, Mar 26, 2012 at 2:13 PM, George Tzotzos <gtzotzos.me.com> wrote:
> BOM_138.O1 SER_56.HG SER_56.OG 452 0.28 2.938 161.198
>
> Using cpptraj with mask definition
>
> hbond out hb.dat :138 dist 3.5 avgout avg.dat
>
> produces NOTHING.
Currently cpptraj uses the mask to search for potential hydrogen bond
donors and acceptors. If you specify only ':138' as your mask you are
searching for donors/acceptors only within residue 138. If you want to
look for hydrogen bonds between residues 138 and 56 you would need to
specify:
hbond out hb.dat :138,56 dist 3.5 avgout avg.dat
Note that the upcoming release of cpptraj will allow much more
flexibility in terms of specifying donor/acceptor atoms through mask
expressions.
Hope this was helpful,
-Dan
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Received on Mon Mar 26 2012 - 12:30:05 PDT
