> I want to know how many water molecules are around a given amide
> hydrogen at a given distance. And do this throughout a trajectory for
> each residue??
Carnal's HBOND allows one to set bond and angle definitions
for hbonds and generate voluminous output showing occupancy
for each step, however the output would need further processing
to get what you want. There is also the DISTRIBUTION RAW DIST
command that would measure all distances between all the H's
of interest and all the waters and dump them for postprocessing.
This sounds like it would be worth adding as a new function
rather than figuring out postprocessing, e.g. in carnal-style
syntax:
OCCUPANCY o1 solute_grp solvent_grp cutoff;
where the solute_grp would be the H's of interest, the solvent_grp
the water O's, and the output would be something like this:
step1 TRP 2 H1: 12
step1 ALA 5 H2: 0
step2 TRP 2 H1: 10
step2 ALA 5 H2: 1
...
This is the sort of functionality I can add on a contract basis
if anyone is interested.
Bill Ross
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Received on Wed Jan 14 2004 - 15:53:10 PST
