Dear Justin<br><br>Thank you so much for help.<br><br>I  used # symbol in where you said and problem was solved. a output was obtained with name summary_HBmap.dat.<br>this file is as follows:<br><br>#    Donor                    Acceptor                % Exist.   <br>
                                                             5.478 <br>      NGL1             N          NGL1            H2         0.040 <br>      LYP2           HB2          LYP2           HG1         0.040 <br>      LYP2             O          GLY3             H         6.158 <br>
      GLN5             N          GLN5            CA         0.040 <br>      GLN5             C          VAL6             N         0.040 <br>      VAL6          3HG2          VAL6             O         0.320 <br>      ARG7           HD2          ARG7            HE         0.040 <br>
      PHE8            HA          PHE8           HB1         8.517 <br>      PHE8             C          SER9             N         1.439 <br>     ASN10            CA         ASN10            CB         0.600 <br>     ASP11            HA         ASP11           HB1         0.040 <br>
     GLN12           HB2         GLN12           HG1         0.440 <br>     THR13            CB         THR13           CG2         3.199 <br>     ILE14            HB         ILE14          1HG2         0.800 <br>     GLU15             H         GLU15            HA         3.798 <br>
     LEU16             H         LEU16            HA         0.040 <br>     LEU16          3HD2         LEU16             O         0.040 <br>     GLU17           OE2         GLU17             O         2.279 <br>     LYP18           HD2         LYP18           HE1        30.508 <br>
     LYP19           HB1         LYP19            CG        23.231 <br>     LYP19             C         PHE20             N         0.840 <br>     PHE20            HZ         PHE20           HE2         0.040 <br>     GLU21           HG1         GLU21            CD         0.480 <br>
     THR22          2HG2         THR22           OG1         4.518 <br>     GLN23           HG2         GLN23           OE1         0.360 <br>     LYP24            CG         LYP24           HG2         0.120 <br>     TYR25             N         TYR25            CA         0.080 <br>
     TYR25           CE2         TYR25           CD2         1.519 <br>     LEU26           CD1         LEU26          2HD1        10.716 <br>     SER27           HB1         SER27            OG         3.958 <br>     PRO28           HB2         PRO28            HA         0.120 <br>
     PRO29            CA         PRO29             C         0.440 <br>     GLU30           OE1         GLU30             C        11.955 <br>                                                            17.193 <br>      NGL1             N                                     5.718 <br>
      GLU30             N                                     7.837 <br>     SER27            OG                                     1.279 <br>     SER27             N                                     6.078 <br>     LEU26             N                                     0.040 <br>
     TYR25            OH                                     0.080 <br>     TYR25             N                                    49.100 <br>     LYP24            NZ                                    89.204 <br>     LYP24             N                                     7.917 <br>
     GLN23           NE2                                    25.590 <br>     GLN23             N                                    73.051 <br>     THR22           OG1                                     1.719 <br>     THR22             N                                    93.882 <br>
     GLU21             N                                     1.839 <br>     PHE20             N                                     0.200 <br>     LYP19            NZ                                     0.040 <br clear="all">
<font color="#888888">
<font color="#888888">
</font></font><br>I have some question: <br><br>1) when I used g_hbond for obtaining hbond.ndx and hbmap.xpm and hbond.log file, I selected two groups(1- protein nad 2- dna).In hbond.log and hbond.ndx file there are acceptors and donors belonging to both of protein and dna, while in my summary_HBmap.dat file both of donors and acceptors only belongs to protein. is there problem?<br>
<br>2) at the end of this file, there are only donors. what is means of %exist for these donors. This file should give me existence of each hbond during my trajectory and not donors.<br><br>3) I think that %exist should be determined for each of donor-hydrogen-acceptor being in hbond.ndx file.Isn&#39;t it?<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>