On Sat, Feb 26, 2011, Sangita Kachhap wrote:
>
> > Yes, because right now your 'acceptor' command is being ignored. The
> > acceptor command assumes that each atom in the first mask (the 'heavy'
> > atom) is bonded to each atom in the second mask (the hydrogen atom);
> > this information is used to calculate angle. Why not specify "acceptor
> > mask :1-24,26-43,45-47,48-57,59-73,75-146.N
> > :1-24,26-43,45-47,48-57,59-73,75-146.H"
>
> I have used these atom mask specification but again getting same warning
>
> PTRAJ: acceptor mask :20-280.N :20-280.H
> Mask [:20-280.N] represents 261 atoms
> Mask [:20-280.H] represents 253 atoms
> WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
> atom selection in the two masks :20-280.N and :20-280.H which contain 261 and 253
> atoms respectively. Ignoring...
It looks like you have 8 prolines in the residues 20-280; these have N but not
H. You will have to use the explicit sort of mask suggested above to skip
them.
....dac
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Received on Sat Feb 26 2011 - 06:30:03 PST
