On 05/02/10 00:43, vivek sharma wrote:
Hi Mark,
Thanks for your response, it worked well for few molecule but not for all.
As I mentioned first I am doing docking and then processing receptor
through pdb2gmx and ligand through PRODRG server.
But number of Hydrogen atoms in docked ligand and PRODRG generated
topology are not same.
Why? How? This must be known to resolve the issue. If the docking
program strips off all hydrogens, then look in its documentation for
methods to build them back in after docking. You must also ensure the
state of titratable groups is consistent.
Although, number of Hydrogens are same in PRODRG
generated topology and pdb file but I can't use them as they have
modified co-ordinate than docked ligand, and the docked ligand
coordinates can't be used as they dont have all Hydrogen atom as
mentioned in topology file (.itp file).
Can you suggest a way to come out of this problem.
Not without more information.
Mark
Thanks & Regards,
Vivek
On 27 January 2010 10:40, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
On 27/01/10 15:58, vivek sharma wrote:
Hi Dallas,
I am trying to run MD simulation over a docked complex
(protein+ligand),
to confirm their dynamic stability in water media.
For the same I am using PRODRG server to generate topologies for
ligand
molecule as gromacs can generate topology for 20 standard
residues. As
mentioned in tutorial for drug-enzyme complex, I am editing the
.top and
.gro files to include the PRODRG generated files (DRGGMX.ITP in
.top and
DRGAPH.GRO in .gro file).
I observe that their are changes in co-ordinate of ligand after
processing them through PRODRG server. So these new co-ordinates for
ligand are placing ligand away from the protein while the ligand
molecule was in protein pocket in original docked complex.
I hope it gives what I am trying to do, and where I am getting
stuck.
I am looking for some suggestions and more insight of the problem to
solve it.
Earlier I have done same procedure successfully for a different
docked
complex.
So you already have the coordinate file from which you wish to begin
MD, and all you need are topologies. One approach is to generate
your ligand .itp file with PRODRG as above, and your protein .top
file with pdb2gmx from the same coordinate file with the ligand
absent. Now you can simply take the protein.top file, #include the
ligand .itp file and amend the [ molecules ] section. This is now a
protein+ligand .top file.
Then you will need to take your original protein+ligand structure
file and perhaps modify the ligand part to conform with the atom and
residue names and ordering in the PRODRG output coordinate file -
but you don't need to concern yourself with the coordinates it produces.
As normal, you will need to take care that the coordinate file you
provide to grompp has the molecules ordered in the same order of the
[molecules] section, and that atoms within molecules have a
corresponding ordering in .top and coordinate file.
Mark
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