I apologise for writing again on the same. I'm a little puzzled using cpptraj to find hbonds
Using it without defining mask:
trajin
hbond out hb.dat dist 3.5 avgout avg.dat
produces an output which contains what I'm looking for. Here's an example:
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.
Your suggestions will be much appreciated
George
On Mar 26, 2012, at 4:26 PM, George Tzotzos wrote:
> I'm new to cpptraj and therefore this may be trivial.
>
> I'm using
>
> cpptraj prmtop hbond.in
>
> whereby hbond.in is:
>
> trajin mdcrd
> hbond out hbond.dat :142 avgout avg.da
>
> It results in two files as expected but no hbonds are shown.
>
> Using ptraj and the same mask I get hbonds with occupancy > 80%
>
> If there's something wrong with the cpptraj syntax, I would be most grateful for your suggestions
>
> Regards
>
> George
>
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Received on Mon Mar 26 2012 - 11:30:03 PDT
