[gmx-users] Problem with g_hbond perl script output

Jacob Babinec jsb332 at drexel.edu
Thu May 8 11:35:49 CEST 2014

Hi GMX-users,

I have been having issues with plot_hbmap.pl because the output it included has none of the residues I am suggesting it to find. I get my hbmap.xpm file by using g_hbond and picking the ligand group first only to receive this output after running perl:

# Donor    Acceptor  % Exist.
 ILE16  N  ILE16  H2  21.956
 ILE16  CD  ILE16  HD2  2.739
 VAL17  3HG1  VAL17  1HG2  13.117
 GLY19  H  GLY19  HA1  0.140
 TRP20  HD1  TRP20  HE1  0.020
 GLU21  N  GLU21  CA  10.238
 CYS22  N  CYS22  CA  2.899
 GLU23  HB1  GLU23  CG  0.040
 LYS24  HB1  LYS24  CG  89.042
 LYS24  C  HIS25  N  0.920
 HIS25  CD2  HIS25  C  53.329
 GLN27  N  GLN27  CA  4.499
 GLN27  C  PRO28  N  1.060
 PRO28  O  TRP29  H  25.635
 TRP29  HZ2  TRP29  HH2  0.020
 GLN30  HB1  GLN30  CG  0.020
 VAL31  HA  VAL31  HB  4.919
 LEU32  CA  LEU32  CB  27.435

I do the opposite and choose the protein first and I get this output:

# Donor    Acceptor  % Exist.
 ILE16  N  ILE16  H2  2.739
 ILE16  CD  ILE16  HD2  89.042
 VAL17  3HG1  VAL17  1HG2  0.920
 GLY19  H  GLY19  HA1  53.329
 TRP20  HD1  TRP20  HE1  4.499
 GLU21  N  GLU21  CA  1.060
 CYS22  N  CYS22  CA  25.635
 GLU23  HB1  GLU23  CG  0.020
 LYS24  HB1  LYS24  CG  0.020
 LYS24  C  HIS25  N  4.919
 HIS25  CD2  HIS25  C  2.899
 GLN27  N  GLN27  CA  27.435
 GLN27  C  PRO28  N  0.160
 PRO28  O  TRP29  H  21.956
 TRP29  HZ2  TRP29  HH2  13.117
 GLN30  HB1  GLN30  CG  0.140
 VAL31  HA  VAL31  HB  0.020
 LEU32  CA  LEU32  CB  10.238

The issue I have with this is the residues given are within the first 32 residues of my protein. My ligand is the last residue (248). Can anybody help guide me to what I am doing wrong?


Jacob Babinec

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