[AMBER] Hbond Difference For Ambertools 12 and 14, or bug

From: <leexa.intern.bii.a-star.edu.sg>
Date: Mon, 22 Sep 2014 14:37:41 +0800

Hi,

I was comparing my Hbond outputs using the Hbond command from both
ambertools12, and ambertools14.
There was discrepency for hydrogen bonding for some types of hydrogen
bonding between them.

1. H of water and O of protein was found to be the same
2. H of bound to O/N of protein and O of water was found to have very
high fractions up to 2.5 compared to an expected maximum of ~1.

Or is there a difference in interpreting the output.


Some outputs

#Acceptor DonorH Donor
Frames Frac AvgDist AvgAng
#Solute-Solvent Hbonds:
#Acceptor
GLU_2.OE1_18 SolventH SolventDnr
23243 3.0991 2.8169 157.2853
GLU_2.OE2_19 SolventH SolventDnr
21296 2.8395 2.8203 156.6572
SolventAcc TYR_44.HH_751 TYR_44.OH_750
19425 2.5900 3.0736 152.8013
SolventAcc THR_3.HG1_33 THR_3.OG1_32
19069 2.5425 3.0785 151.2533
SolventAcc TYR_77.HH_1286 TYR_77.OH_1285
18900 2.5200 3.0741 152.3399
SolventAcc LYS_71.HZ1_1170 LYS_71.NZ_1169
18278 2.4371 3.1271 145.4819
SolventAcc LYS_71.HZ2_1171 LYS_71.NZ_1169
17991 2.3988 3.1269 145.6328
SolventAcc LYS_71.HZ3_1172 LYS_71.NZ_1169
17884 2.3845 3.1298 145.6529
SolventAcc TYR_81.HH_1357 TYR_81.OH_1356
17791 2.3721 3.0622 151.3745

Attached is the relevant files.
A view of the trajectory in VMD shows hydrogen bonding to only 1 water
O by the H most of the time, not 2.5 .


Lee Xiong An





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Received on Mon Sep 22 2014 - 00:00:02 PDT
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