Dear Amber users,
I am trying to use CPPTRAJ hbond module for the hydrogen bond calculation.
The AmberTools-12 manual ( page number 187-188) says that 'hbond' module
will calculate the distance between the heavy atoms and also - “hydrogen
bonds are FON”. But, when I look into the output of my Hbond analysis, I
could not able see that the calculation maintain these criteria. My output
look like as shown below
***************************************************************************************************************
#Acceptor DonorH Donor Frames Frac
AvgDist AvgAng
LEU_99.HB3 ARL_294.H27 ARL_294.C19 712 0.2848
3.2488 143.3260
HIE_266.HE1 ARL_294.H22 ARL_294.C17 680 0.2720
3.2670 135.8800
LEU_68.HG ARL_294.H37 ARL_294.C23 572 0.2288
3.3155 151.5074
LEU_68.HG ARL_294.H32 ARL_294.C21 537 0.2148
3.2713 138.6602
LEU_270.HA ARL_294.H24 ARL_294.C18 514 0.2056
3.2753 144.5713
LEU_270.HA ARL_294.H25 ARL_294.C18 473 0.1892
3.2773 145.2383
****************************************************************************************************************
Here is the input script I used.
################################################################################
trajin ../../md4.crd
center :1-293 mass origin
image origin center
hbond lig_donor out hb_LIG_donor.dat angle 120 dist 3.5 donormask :294
acceptormask
:25,64,65,67,68,69,70,99,102,103,105,106,109,110,140,143,144,147,158,160,165,167,180,182,183,186,266,267,269,270,273,279,284,288
avgout hb_LIG_donor_avg.dat
############################################################################################################################################
Why hydrogen atoms are considered in the acceptor?. Does the calculation
looking for the H....H-Donor distance here (manual says distance between
heavy atoms)?. Why carbon atoms are considered here, evnethough the
critirion is "“hydrogen bonds are FON” ?
Waiting for the your valuable reply.
Thanks in advance
Anu
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Received on Thu Aug 15 2013 - 00:30:03 PDT
