AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Thomas Cheatham (
Date: Thu Oct 05 2006 - 10:21:40 CDT

> i tried all the modifications Thomas suggested.. but was unable to extract
> any solution to the problem.

The previous PDB file has residues named "DT" instead of "THY". What
residue names are in the prmtop you are using?

Did you try setting prnlev 3 to see what atoms are indeed selected? Or
did you try the "checkmask" command in rdparm?

> i feel that the parser is doing the following at the moment :
> only the first 'THY' or 'GUA' is unrecognized and all the N3 atoms in the
> DNA sample under consideration are listed. as a result there is a mismatch
> in the number of N3 and H3 containing residues. the command i used in the
> .in file for ptraj which strike me as doubtful in terms of syntax is :
> acceptor mask :THY_at_N3 :THY_at_H3
> acceptor mask: :GUA_at_N1 :GUA_at_H1

You need to "show us" what the parser is doing, not what you feel it is
doing. Note that there are two ":"'s in the GUA spec above.

rdparm prmtop
checkmask :THY_at_N3

What does that return?

You can send me your prmtop if you want me to track it down.

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