[gmx-users] several questions about g_hbond -contact

[Anna Marabotti]

Dear users,
I'm using g_hbond with option -contact in order to find the contacts between
my protein and a series of ligands, in a radius of 0.5 nm. I made several
calculations but I'm quite uncertain about the results, therefore I'm asking
you some questions.
 
The command I used is:
g_hbond -f my_prot.xtc -s my_prot.tpr -n index.ndx -g logfile.log -num
contact_num.xvg -hbn contact.ndx -hbm contact.xpm -contact (for options -r
and -r2 see below).
 
Here my questions:
1) I have to indicate two groups when prompted. If I select first "1"
(protein) and then "15" (ligand), the program does not find contacts (it
calculates, but says "No contacts found"). On the contrary, if I first
select "15" and then "1", the program finds contacts. Why? I'm expecting
that if an atom of the protein contacts an atom of the ligand, it is a
reversible thing, especially because this is not a H-bond in which the
different order D-A could affect the results.
To proceed with my test, I always selected first "15" and then "1".
 
2) If I fix only -r 0.5, the program starts calculating. It finds a number
of "donor" and "acceptor" atoms and starts doing a grid search on a 18x18x13
grid, with rcut=0.5. It calculates for all the frames of the trajectory,
then at the end it finds a number of "hbonds" and 0 different atom-pairs
within H-bond distance. At the end, I obtain a range checking error:
"Variable y has value 0. It should have been within [ 0 .. 0 ] and the files
.xvg, .log and .ndx are created, but the file .xpm is not.
If I understand well, the -r2 flag is then absolutely necessary to tell the
program that it does not have to treat this as an H-bond search, but as a
contact search, right? The -contact flag is not sufficient, alone?
 
3) If I fix -r 0.5 -r2 0.6, the program starts calculating. It finds the
same number as above of "donor" and "acceptor" atoms and starts doing a grid
search on a 15x15x11 grid with rcut=0.6. It calculates for all the frames of
the trajectory, then at the end it finds a number of "contacts" and a number
of different atom-pairs within second cutoff distance. It produces all the
files (.xvg, .ndx, .log and .xpm).
In this case, the program has indeed calculated the "contacts", instead of
the "hbonds". However, I don't understand if it calculates the contacts
within a cutoff distance of 0.5 or within a cutoff distance of 0.6 nm. If I
change this second value to, say, 1 nm, the number of contacts is still the
same, but the number of different atom-pairs increases to 15951, and the
grid has different dimensions (9x9x6)
In this case, my question is: how the -r2 flag affects the number of
contacts to find? (I would like to ask: what is the function of flag -r2?
but looking at the gmx-users archive, it seems to me that nobody knows
it...and I'm not able to look into the code, as suggested by somebody...)
 
My final question is, obviously: what is the correct command to provide to
obtain what I want, i.e. the number of contacts between the protein and the
ligand within a cutoff radius of 0.5 nm?
 
Thanks in advance for your suggestions, and best regards
Anna
 
__________________________________________________________________
Anna Marabotti, Ph.D.
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
(Roberto Benigni, about Roberto Saviano)
 
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