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
hbond
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
while
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,
Thomas
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Received on Sun Jul 09 2006 - 06:07:16 PDT
