AMBER: Problem with donor/acceptor specification in ptraj hbonding facilities

From: Thomas Steinbrecher <>
Date: Thu, 6 Jul 2006 16:02:19 -0700 (PDT)

Dear amber users,

while trying to perform H-bonding analysis with the ptraj h-bonding
facility in amber 9 (bugfixes applied) I ran into problems specifying the
donor and acceptor atoms. The manual states there are two ways to do this,
but when specifying donors and acceptor in the <resname> <atomname>
fashion, ptraj seems to ignore my input. Lines in the input file like

         donor ADE N1
         acceptor ADE N6 H61
         acceptor ADE N6 H62

resulted in output of

         PTRAJ: donor ADE N1

         PTRAJ: acceptor ADE N6 H61

         PTRAJ: acceptor ADE N6 H62

without the usual message of how many atoms were found. The
following commands

         donor print
         acceptor print

result in

         PTRAJ: donor print

         PTRAJ: acceptor print

         PTRAJ: hbond
         WARNING in ptraj(), hbond: No list of hbond donors/acceptors has been
         specified. Ignoring command...
         [No output trajectory specified (trajout)]

and consequently, no hbond analysis is performed. The other way of
specifying donors and acceptor in the form of

         donor mask :1.N1

gives the expected output

         PTRAJ: donor mask :1.N1
         Mask [:1.N1] represents 1 atoms


         donor mask :ADE.N1

selects all atoms named N1, even if their resname is not ADE.

I have looked into the code, the functions parseHBondDonor and
parseHBondAcceptor seem to contain both the possibility of specifying
hbonds as masks and in the <resname> <atomname> fashion, but it looks like
the second option does not work for me.

Does anyone have experience with using the donor/acceptor commands that
might help me here?

Kind Regards,

The AMBER Mail Reflector
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Received on Sun Jul 09 2006 - 06:07:16 PDT
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