On Fri, Jun 6, 2014 at 2:51 AM, Arunima Shilpi <writetoash28.gmail.com>
wrote:
> Here for hbond analysis I used the following input file
>
>
> trajin md2.mdcrd
>
>
> donor :MET50.H
>
These masks are wrong. You can specify residue names OR residue numbers.
But not both.
> donor :PHE453.H
> donor :GLY455.H
> donor :GLY457.H
> [snip]
>
>
> hbond distance 3.5 angle 120.0 includeself donor acceptor neighbor 2 series
>
> While running the command
>
> prtaj 3pta_DRG_solvated.top <ptraj_hbond.in>ptraj_hbond.out
>
> I got the following error
>
> PTRAJ: acceptor :ASP498.OD2
> WARNING in ptraj, acceptor: error in specification of res/atom selection
>
This tells you that your acceptor mask did not match any atoms, indicating
there is a problem with your mask. The Amber manual has a description of
the mask syntax.
Also, it may be worth looking into the hbond command in cpptraj instead
(which typically eliminates the need to set a list of donors and
acceptors). This is described in the manual as well.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Jun 06 2014 - 05:30:02 PDT
