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 mohsen
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