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

[Justin A. Lemkul]

Quoting leila karami <karami.leila1 at gmail.com>:

> 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.
>                                                              5.478
>       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
>                                                             17.193
>       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.
>

Your output is total nonsense.  Please refer to the header of the script for
proper input.  I suspect the problem is with the index file.  You should NOT
pass the entire hbond.ndx file to the script.

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

It is, provided you pass proper input to the script.

-Justin

> --
>
> 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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