> donor mask :ADE.N1
> *acceptor mask :THY.N3 :THY.H3*
> hbond distance 7 series hbond
> trajout traj.peptide nobox
>
> the output (only that part showing the error) was as follows:
>
> PTRAJ: acceptor mask :THY.N3 :THY.H3
> Mask [:THY.N3] represents *84 atoms*
> Mask [:THY.H3] represents 18 atoms
> WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
> atom selection in the two masks :THY.N3 and :THY.H3 which contain 84 and 18
> atoms respectively. Ignoring...
OK, my educated guess is that the mask is not being interpreted properly
and in fact is not treating the :THY match correctly (instead matching all
residues). This should not happen, but may be happening since you do not
have any THY residues. According to your PDB file you have residues "DT".
Try
prnlev 3
acceptor mask :DG.N1 :DG.H1
prnlev 0
Also, there is a nice command called "checkmask" in rdparm what allows you
to interactively test various mask specifications to see if they return
what you expect...
You could also try
acceptor DG N1 H1
Finally, in the hbond specification above,
> hbond distance 7 series hbond
do you want angles? If not, set angle negative; do you want output?
hbond series hbond out hbond.dat distance 7.0 angle -1.0
Note that as ptraj is started up, it outputs the names of the residues in
the prmtop; make sure you are using these for the atom selections. I'll
dig into the poor matching with ":THY", ":GUA", etc.
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Received on Sun Oct 08 2006 - 06:07:11 PDT
