Hi Nataraj,
this happened to me also.
When you make an energy minimization, gromacs alters the coordinates of
your protein. When you place the ligand back to the gro file, it will be
placed far from its site. To solve this problem I take the original
complex and fit it to the minimized protein (using DeepView or any other
program like Whatif, for example), then save only the ligand of the
complex and use these new coordinates to feed the gro file of the
minimized protein.
Hope I understood your problem.
All the best
Alberto
raja wrote:
Dear Tsjerk,
Thanks for your prompt replies, But please bit elaborate your
answer. Yea I do use editconf
for the purpose of renumbering ligand after pasted in original protein
gro file produed by pdb2gmx step (as per my previous mail). But where
come the option of -s in ediconf as you mentioned in your earlier mail
".... If you place your ligand (-s first atom)".
Please mention the exact command to position the ligand in its original
place using editconf. More I would like to add more observation , during
the process of these preparation of protein-enzyme complex, upto grompp
for em file, the added ligand atoms are appears to be distorted but at
the end of the energy minimization, the original molecules of ligand is
restored.(may be this is not my concern rightnow,so please give me
elaborate command to position the ligand in its active site)
With thanks !
B.Nataraj
On Wed, 22 Mar 2006 14:31:42 +0100, "Tsjerk Wassenaar"
<[EMAIL PROTECTED]> said:
Hi Raja,
When you generate a .tpr file (for whatever purpose) all molecules will
be
mapped to a rectangular box as good as possible. For this, the first atom
of
the molecule is used. So when a molecule happens to be sticking out of
the
rectangular box, or when it is just pushed over the border during EM/PR,
it
will be mapped to the other side and it will appear to have jumped. If
you
place your ligand (-s first atom) in the center of the rectangular box
(editconf -c), it will stay there during EM/PR.
Cheers,
Tsjerk
On 3/22/06, raja <[EMAIL PROTECTED]> wrote:
Dear Tsjerk,
Thanks for your reply. But I have not gone to the stage of
dynamics yet. I am still struck at energy minimization. Now
atleast I could reason out why it happens, but I dont know how
to stop it. The reason is everytime
when I convert ligand-enzyme complex using pdb2gmx, I trim off the
ligand and convert the protein part alone, later I
paste the drug molecule in the resultant file. I suspect that could be
the problem,so I try to fix it by myself.
With thanks !
B.Nataraj
On Wed, 22 Mar 2006 07:54:05 +0100, "Tsjerk Wassenaar"
<[EMAIL PROTECTED]> said:
Hi Raja,
Probably PBC. Nothing wrong, just visual. You can try to center your
system
on the ligand before starting the simulation, which should keep it "in
place".
Tsjerk
On 3/22/06, raja <[EMAIL PROTECTED]> wrote:
Dear GMXIONS,
I reposting the same query since not getting response for my previous
posting. In short
I am unable to restraint the ligand at its active site during
minimization, though I used position restrints
for all of the atom types of my ligand. At the end of simulation, it
is
jumping out of active site and located
itself at the corner of the water box.
Kindly provide me the solution to retain the ligand at its original
position during minimization step!
With thanks !
B.Nataraj
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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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