[gmx-users] Problem with g_hbond perl script output

[Justin Lemkul]

On 5/8/14, 5:14 AM, Jacob Babinec wrote:
> 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.
>           0.160
>   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.
>           0.040
>   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?
>

Something more fundamental is wrong here; most of the listed interactions aren't 
even hydrogen bonds.  Likely something is wrong with the index group you are 
providing to plot_hbmap.pl.  Since this isn't an actual Gromacs problem (or 
Gromacs software at all), you can email me off-list to diagnose this.  If you 
provide me with all of your input files, I can figure out what's going on.  Just 
by looking at the output, though, it is almost certain that something is screwy 
with the hbond.ndx file you're giving it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================