Dear Amber Users
I used the following command to find the H bond between two bases i.e
Guanine and Cytosine
hbond out hb.dat :1,6 dist 2.5 avgout avg.dat
I got the following dat :
#Acceptor DonorH Donor Frames Frac AvgDist
AvgAng
RC3_6.N3 RG5_1.H1 RG5_1.N1 992 0.9920 3.0329
162.1346
RC3_6.O2 RG5_1.H21 RG5_1.N2 976 0.9760 2.9256
162.4696
RG5_1.O6 RC3_6.H41 RC3_6.N4 893 0.8930 2.9950
160.9051
RC3_6.O2 RG5_1.H1 RG5_1.N1 292 0.2920 3.2799
141.3739
RC3_6.N3 RG5_1.H21 RG5_1.N2 25 0.0250 3.3991
139.3231
RC3_6.N4 RG5_1.H1 RG5_1.N1 7 0.0070 3.3845
137.8618
RG5_1.N1 RC3_6.H41 RC3_6.N4 7 0.0070 3.4564
140.1925
RC3_6.O2 RC3_6.HO'2 RC3_6.O2' 2 0.0020 3.2341
139.4926
RC3_6.O3' RC3_6.HO'2 RC3_6.O2' 2 0.0020 2.5560
137.4556
Then I gave the command to find the hydrogen bond of the two adjacent
Guanine and cytosine pair
hbond out hb.dat :1,6 :2,5 :3:4 dist 2.5 avgout avg.dat
But the results showed the same as the above dat file.
Where did the script go wrong?
Thanks in advance
Martina
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Received on Thu Jul 13 2017 - 09:30:02 PDT
