[gmx-users] H-bond calculation
rajiv at kaist.ac.kr
Wed Sep 16 08:39:37 CEST 2015
I would like to calculate the H-bond occupancy between two residue (intra mol inter Thr183 (OG1) -Tyr162 (N) ).
I made a .ndx file choosing the both atoms : Group 40 ( r_162_&_N) has 1 elements
Group 41 ( r_183_&_OG1) has 1 elements
and given the " gmx hbond -f prd_noPBC.xtc -s em.tpr -n index.ndx -dist hbdist.xvg -hbn hbond.ndx -hbm hbmap.xpm -tu ns "
but they end up in error as follows: Found 0 donors and 2 acceptors
Making hbmap structure...done.
No Donors found.
I wonder how can i calculate the intra molecular residue-residue hydrogen bond over time as well as their occupancy in percentage? Thanks.
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