[gmx-users] %exist hydrogen bond - difference between number of lines in input and output files
leila karami
karami.leila1 at gmail.com
Thu Feb 24 14:58:48 CET 2011
Dear Justin
I have a question about output file (summary_HBmap.dat).
my input file (hbound.ndx) is as follows:
[ hbonds_Protein-ab_interfacial ]
1019 1021 13088
1019 1021 23621
1016 1018 23621
1013 1014 12392
1013 1014 23621
992 994 12392
946 949 23621
853 855 6251
853 855 15473
777 780 15473
777 780 23621
723 725 15473
720 722 15473
504 506 23621
501 503 23621
98 100 7952
98 100 15473
92 93 7952
79 80 7952
58 60 15473
46 47 7952
46 47 15473
39 40 18725
6251 6252 796
6251 6252 866
6251 6252 867
7952 7953 62
12392 12393 857
12392 12393 919
12392 12393 920
13088 13089 857
13088 13089 858
13088 13089 866
15473 15474 57
15473 15474 62
15473 15474 701
15473 15474 703
18725 18726 45
18725 18726 62
18725 18726 63
19556 19557 744
19556 19557 797
23621 23622 866
23621 23622 871
23621 23622 1041
It contains 45 lines showing hydrogen bonds.
my out put file is as follows:
# Donor Acceptor % Exist.
0.400
ARG58 NH2 SOL3827 OW 43.565
ARG58 NH2 SOL7338 OW 21.663
ARG58 NH1 SOL7338 OW 0.160
ARG58 NE SOL3595 OW 1.359
ARG58 NE SOL7338 OW 59.233
ARG57 NH1 SOL3595 OW 0.480
LYP55 NZ SOL7338 OW 98.002
GLN50 NE2 SOL1548 OW 1.359
GLN50 NE2 SOL4622 OW 0.080
LYP46 NZ SOL4622 OW 0.480
LYP46 NZ SOL7338 OW 0.320
ARG43 NH2 SOL4622 OW 0.320
ARG43 NH1 SOL4622 OW 0.160
ARG31 NH2 SOL7338 OW 0.240
ARG31 NH1 SOL7338 OW 16.147
ARG7 NH2 SOL2115 OW 3.277
ARG7 NH2 SOL4622 OW 50.679
ARG7 NE SOL2115 OW 0.320
ARG7 N SOL2115 OW 0.719
GLN5 NE2 SOL4622 OW 0.320
GLN5 N SOL2115 OW 32.534
GLN5 N SOL4622 OW 78.497
GLY4 N SOL5706 OW 0.400
SOL1548 OW THR47 O 61.711
SOL1548 OW ASN51 OD1 16.867
SOL1548 OW ASN51 ND2 95.044
SOL2115 OW GLN5 O 16.147
SOL3595 OW GLN50 O 0.080
SOL3595 OW ARG53 O 0.080
SOL3595 OW ALA54 N 3.118
SOL3827 OW GLN50 O 0.080
SOL3827 OW ASN51 N 33.253
SOL3827 OW ASN51 OD1 0.560
SOL4622 OW GLN5 OE1 1.279
SOL4622 OW GLN5 O 0.080
SOL4622 OW GLU42 OE2 0.080
SOL4622 OW GLU42 O 2.798
SOL5706 OW GLY4 O 0.080
SOL5706 OW GLN5 O 0.080
SOL5706 OW VAL6 N 96.003
SOL5983 OW GLN44 O 0.160
SOL5983 OW TRP48 N 0.160
SOL7338 OW ASN51 OD1 0.320
SOL7338 OW ASN51 O 0.080
It contains 44 lines showing hydrogen bonds and 45 lines showing % exist.
I want to know reason this difference in number of lines.
and also I want to know what is 0.400 in second line of output file?
at the end of input file, there is 3 lines
23621 23622 866
23621 23622 871
23621 23622 1041
corresponding to SOL7338, but at the end of output file, there is 2 lines
SOL7338 OW ASN51 OD1 0.320
SOL7338 OW ASN51 O 0.080
please explain this differences more.
best regards.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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