[gmx-users] Docking

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Apr 27 11:05:04 CEST 2011

Dear Users

I read so many emails to mailing list, there were important notes about
docking but I couldn't extract a general result.
Please let me know:

1-Can we dock a ligand to it's protein's binding pocket with Pymol and
Gromacs as following?

first:locating ligand outside and close to binding site  manually in pymol
and saving complex.pdb
second:doing all steps for generating complex.top and complex.gro as
Enzyme-Drug tutorial
third:running md (with out any pull code and constraint),in the other
words,full flexible system.

I think drug can move freely and according to it's interaction with binding
site can be attracted by binding site.
reside for a distance time and then will come out of pocket.

Am I right?
I know what discussed in mainling list about deffinition of "Docking".

2-I have some docked files by "Docking Server " for some of my
drug-protein's complexes.
now,I want to obtain them by doing MD in the above proccess.if I was
successful then try to do that for other drugs which I don't have any docked
pdb for them.

How can I fit a trajectory with a typical pdb file?

Thanks in advance for any idea
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