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