Dear Amber Users
I have a system consisting of ions (A) and water (W) that hydrogen between
one another. I wanted to specifically calculate various kinds of bridges
formed by water:
A-W-A: where the water bridges between two ions
A-W-W: where the water bridges between an ion and another water
W-W-W: where the water bridges between two waters.
I used the following cpptraj commands for the same:
hbond A_W solventdonor :WAT solventacceptor :WAT :A angle 135.0 dist 3.5
nointramol bridgeout watbridge.dat
hbond A_W1 solventdonor :WAT solventacceptor :WAT acceptormask :A,:WAT
donormask :WAT angle 135.0 dist 3.5 nointramol bridgeout watbridge1.dat
hbond W_W solventdonor :WAT solventacceptor :WAT acceptormask :WAT
donormask :WAT angle 135.0 dist 3.5 nointramol bridgeout watbridge2.dat
run
writedata A_W_bridge.dat A_W[Bridge]
writedata A_W_bridge1.dat A_W1[Bridge]
writedata W_W_bridge.dat W_W[Bridge]
I presumed that A_W_bridge1.dat will have information about A-W-W as well
as A-W-A (since both A and WAT are mentioned in the solute mask) and will
actually be a sum of the information in A_W_bridge.dat (has only A in the
solute mask) and W_W_bridge.dat (has only WAT in the solute mask.
However, this doesn't seem to be the case. The W_W_bridge.dat has far more
number of W-W-W bridges recorded than A_W_bridge1.dat.
Where am I going wrong?
Thanks in advance for any suggestions
--
Debostuti
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Received on Wed Jun 24 2015 - 07:00:03 PDT
