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>