[gmx-users] %exist hydrogen bond - difference between number of lines in input and output files
Justin A. Lemkul
jalemkul at vt.edu
Thu Feb 24 15:01:58 CET 2011
leila karami wrote:
> 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.
>
Your .ndx file should not contain the directive heading. Per the instructions
in the header of the .pl script: "bond.ndx (modified to contain only the atom
numbers in the [hbonds...] section, nothing else)"
-Justin
> best regards.
>
>
>
>
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
>
> Theoretical Physical Chemistry Group
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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