[gmx-users] perl script for g_hbond / summary_HBmap.dat

leila karami karami.leila1 at gmail.com
Wed Nov 24 09:24:30 CET 2010

Dear Justin

Thank you so much for help.

I  used # symbol in where you said and problem was solved. a output was
obtained with name summary_HBmap.dat.
this file is as follows:

#    Donor                    Acceptor                % Exist.
      NGL1             N          NGL1            H2         0.040
      LYP2           HB2          LYP2           HG1         0.040
      LYP2             O          GLY3             H         6.158
      GLN5             N          GLN5            CA         0.040
      GLN5             C          VAL6             N         0.040
      VAL6          3HG2          VAL6             O         0.320
      ARG7           HD2          ARG7            HE         0.040
      PHE8            HA          PHE8           HB1         8.517
      PHE8             C          SER9             N         1.439
     ASN10            CA         ASN10            CB         0.600
     ASP11            HA         ASP11           HB1         0.040
     GLN12           HB2         GLN12           HG1         0.440
     THR13            CB         THR13           CG2         3.199
     ILE14            HB         ILE14          1HG2         0.800
     GLU15             H         GLU15            HA         3.798
     LEU16             H         LEU16            HA         0.040
     LEU16          3HD2         LEU16             O         0.040
     GLU17           OE2         GLU17             O         2.279
     LYP18           HD2         LYP18           HE1        30.508
     LYP19           HB1         LYP19            CG        23.231
     LYP19             C         PHE20             N         0.840
     PHE20            HZ         PHE20           HE2         0.040
     GLU21           HG1         GLU21            CD         0.480
     THR22          2HG2         THR22           OG1         4.518
     GLN23           HG2         GLN23           OE1         0.360
     LYP24            CG         LYP24           HG2         0.120
     TYR25             N         TYR25            CA         0.080
     TYR25           CE2         TYR25           CD2         1.519
     LEU26           CD1         LEU26          2HD1        10.716
     SER27           HB1         SER27            OG         3.958
     PRO28           HB2         PRO28            HA         0.120
     PRO29            CA         PRO29             C         0.440
     GLU30           OE1         GLU30             C        11.955
      NGL1             N                                     5.718
      GLU30             N                                     7.837
     SER27            OG                                     1.279
     SER27             N                                     6.078
     LEU26             N                                     0.040
     TYR25            OH                                     0.080
     TYR25             N                                    49.100
     LYP24            NZ                                    89.204
     LYP24             N                                     7.917
     GLN23           NE2                                    25.590
     GLN23             N                                    73.051
     THR22           OG1                                     1.719
     THR22             N                                    93.882
     GLU21             N                                     1.839
     PHE20             N                                     0.200
     LYP19            NZ                                     0.040

I have some question:

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?

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.

3) I think that %exist should be determined for each of
donor-hydrogen-acceptor being in hbond.ndx file.Isn't it?


Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101124/0f70e06d/attachment.html>

More information about the gromacs.org_gmx-users mailing list