AMBER Archive (2006)

Subject: Re: AMBER: ptraj hbond analysis troubles

From: Sayandeep Purkayasth (
Date: Thu Oct 05 2006 - 08:37:07 CDT

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

in most cases where the old mask syntax was used, the parser was unable to
recognise the command. whereas in the cases of the new syntax (as in ambmask
syntax) ptraj continued to return the same errors in case of THY and GUA
only. this is unexpected since with the other bases no such problem is seen.

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

i repeated the ptraj analysis with another prmtop with A-T, G-C base pairing
as opposed to the previous case, yet the error persisted.

i feel there is some error in the parser. however being new to this package,
i cannot tell for sure. can someone please post a solution. i have looked up
the archives and seen some similar problems which were not properly dealt

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