Hi all,
I am trying to use the hbond utility and determine the possible
hydrogen bonds between protein residue and
water (SPC).
I try defining the acceptor
acceptor mask :1496-6496.O=,H=
or even
acceptor mask :SPC.O=,H=
or
acceptor SPC
while executing this line it doesnt seem to detect the atoms and says
"WARNING in ptraj, acceptor: Error in mask specification. Ignoring..."
It seems to be giving me an output with the possible water
interactions with protein residue but I am worried about the warning.
Could some please help.
thanks,
ganesh
SCRIPT
trajin mdcrd
center origin
image origin center
acceptor mask :1496-6496.O=,H= *****SPC water******
donor mask :1321-1481.N=,O=,S= *****protein residues*****
hbond series hbt angle 120.0 distance 3.5 solventneighbor 100
solventdonor SPC O solventacceptor SPC O H1 solventacceptor SPC O H2
hbfile hbond_time.dat avgfile average_stat.dat solventhbonds >EOF
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Received on Mon May 17 2010 - 14:30:03 PDT
