Hello,
I am trying to specify the donor and acceptor mask for hbond analysis. I
tried the selection in two ways (pasted below). In both cases ptraj dose not
recognize the acceptors & i dnt understand the mistake. Kindly write me
what is going wrong.
As per ambertools manual, the syntax is
acceptor resname atomname atomnameH | mask mask maskH | clear | print
I just want to select ARG in the resid range 149-183 and the corresponding
hydrogens bonded to NH1 atom of ARG.
1)
donor mask :149-183.OD1
donor mask :149-183.OE1
acceptor mask :149-183.1HH1
acceptor mask :149-183.2HH1
2)
donor mask :149-183.OD1
donor mask :149-183.OE1
acceptor mask :149-183.NH1,1HH1
acceptor mask :149-183.NH1,2HH1
PTRAJ: rms reference out X4U_V3.rms :149-183.CA,C,N
Mask [:149-183.CA,C,N] represents 105 atoms
PTRAJ: donor mask :149-183.OD1
Mask [:149-183.OD1] represents 3 atoms
PTRAJ: donor mask :149-183.OE1
Mask [:149-183.OE1] represents 1 atoms
PTRAJ: acceptor mask :149-183.NH1,1HH1
WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
PTRAJ: acceptor mask :149-183.NH1,2HH1
WARNING in ptraj, acceptor: Error in mask specification. Ignoring...
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Received on Tue Sep 27 2011 - 11:30:03 PDT
