Hi everyone,
I want to identify water molecules which satisfy all these three
conditions.
1) Within 3.5 Angstrom from Gamma phosphate (PG) of GTP (:173)
2) Makes hydrogen bond with OE1 atom of Q61 residue
3) Angle between O of the water, :173.PG (PG of GTP) and :173.O3B
(O3B of GTP) is >= 140 degrees
I tried the following but I don't think it is working.
hbond HB_Q61_WAT donormask :WAT.O acceptormask :61.OE1 distance 3.5 angle
135 out HB_Q61_WAT.dat
distance O_WAT_PG :WAT.O :173.PG out nuc_dist.dat
angle nuc_angle :WAT.O :173.PG :173.O3B out nuc_angle.dat
I am not sure if I am getting the right nuc_dis.dat and nuc_angle.dat
Can anyone help me with this.
Regards
Abhilash
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Received on Mon Jan 05 2026 - 13:30:13 PST
