Dan,
Many thanks. The use of mask in cpprat hbond is now clearer to me.
Regards
George
On Mar 26, 2012, at 9:06 PM, Daniel Roe wrote:
> 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 - 12:30:06 PDT
