First thank you for your help and information. Can I
clarify this question: Are the water mediated hbonds still
counted as one per hbonded water in the number of hbond as a function
of time? For example suppose I want to see number of hbonds
from protein sidechains to sidechains and choose water for -ins, are
the water mediated hbonds still counted in the number of hbonds as a
function of time though their atome index are not listed in the file
insert.dat or hbond.ndx? I see these lines around line 1988 are
not commented out:<br>
-----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
if (ins_d && ins_a && ihb) {<br>
/* add to hbond index if not already there */<br>
add_hbond(hb,ins_d_k,ins_a_k,h,grI,ogrp,<br>
nframes,TRUE,bMerge,ihb);<br>
-----------------------------------------------------------------------------------------------------------------------------------------------------------<br>
Is it possible they are still counted in the number
of hbonds as function of time graph (hbnum.xvg)? Or they
are not counted in currently untill the bug is cleared. Thank you
for your help and sorry for taking your time. <br>
<br>
Sincerely<br>
Lydia<br>