Dear Users<br><br>I read so many emails to mailing list, there were important notes about docking but I couldn't extract a general result.<br>Please let me know:<br><br>1-Can we dock a ligand to it's protein's binding pocket with Pymol and Gromacs as following?<br>
<br>first:locating ligand outside and close to binding site manually in pymol and saving complex.pdb<br>second:doing all steps for generating complex.top and complex.gro as Enzyme-Drug tutorial<br>third:running md (with out any pull code and constraint),in the other words,full flexible system.<br>
<br>I think drug can move freely and according to it's interaction with binding site can be attracted by binding site.<br>reside for a distance time and then will come out of pocket.<br><br>Am I right? <br>I know what discussed in mainling list about deffinition of "Docking".<br>
<br><br>2-I have some docked files by "Docking Server " for some of my drug-protein's complexes.<br>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.<br>
<br>How can I fit a trajectory with a typical pdb file?<br><br>Thanks in advance for any idea<br>mohsen<br>