AMBER Archive (2006)

Subject: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?

From: j j (fantvamp_at_gmail.com)
Date: Fri Dec 01 2006 - 04:51:06 CST

I trying to track some ions interactions by using the hbond facility in
ptraj.
To simplify input I've just wrote the essential commands to test:
ptraj prmtop << EOF
# system: 7mer peptide in a box of periodic water (1577 Waters)
# Read in the trajectory file starting at 1, 100 total snapshots
# consider each 10
trajin trj.5 1 100 10
# now do some H-Bond analysis specify the electron pair DONOR
donor mask :1-7_at_O
# specify the ACCEPTOR(s)
acceptor WAT O H1
#acceptor WAT O H2
# do the Hbond search/output
#hbond solventacceptor O H1 solventacceptor O H2 solventneighbor 2 series
hbond
hbond
go
EOF
http://amber.ch.ic.ac.uk/tutorials/basic/tutorial5/index.html
(simplified). This seems to work fine: ptraj_test_OK.out
In the A8 manual treats the case of ions interactions by specifying twice
the atoms
to probe.
Page 211 [..]
The acceptor command is similar except that both the heavy atom and the
hydrogen
atom are specified. If the same atom is specified twice (as might be the
case to
probe ion interactions) then no angle is calculated between the donor and
acceptor.
[..]
For my case, the only results obtained (ptraj_names.in; ptraj_mask.in) are:
 tail -5 ptraj_names.out ptraj_mask.out
==> ptraj_names.out <==
      Hydrogen bond information dumped for occupancies > 0.00

        DONOR ACCEPTORH ACCEPTOR
  atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied
distance angle
 ---------------- ---------------------------------
-------------------------------------

==> ptraj_mask.out <==
      Hydrogen bond information dumped for occupancies > 0.00

        DONOR ACCEPTORH ACCEPTOR
  atom# :res_at_atom atom# :res_at_atom atom# :res_at_atom %occupied
distance angle
 ---------------- ---------------------------------
-------------------------------------
the inputs given:
==> ptraj_names.in <==
trajin ions2test.trj.gz
donor mask :1-76_at_O1P
donor print
#acceptor mask :77-86_at_MG :77-86_at_MG
acceptor MG MG MG
acceptor print
hbond
go
==> ptraj_mask.in <==
trajin ions2test.trj.gz
donor mask :1-76_at_O1P
donor print
acceptor mask :77-86_at_MG :77-86_at_MG
#acceptor MG MG MG
acceptor print
hbond
go

I'm a bit lost here, then,
How can I specify an input for hbond to probe ions interactions?.
Thank you,
JJ



  • application/octet-stream attachment: ptraj.in2




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