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<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>Dear
users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>The command I used
is:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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).</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>Here my
questions:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>To proceed with my
test, I always selected first "15" and then "1".</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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.</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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).</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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...)</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>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?</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012></SPAN></FONT> </DIV>
<DIV><FONT size=2 face=Arial><SPAN class=318405816-21022012>Thanks in advance
for your suggestions, and best regards</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=318405816-21022012>Anna</SPAN></FONT></DIV>
<DIV><SPAN class=318405816-21022012><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=318405816-21022012></SPAN><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>(Roberto Benigni, about Roberto
Saviano)</FONT></DIV></DIV>
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