[gmx-users] on md of protein-ligand

[Brett]

Dear All,


I am learning the md of protein-ligand based on the Justin on-line tutorial. My first question is, for the topology files we need to produce the protein part and ligand part separately, and the input for pdb2gmx did not contain the ligand part. After I got the ligand files, I find the coordinate of the ligands was different from the ligand pdb in the protein-complex pdb (although the rmsd between the ligand topology and the ligand in the complex was 0). Then during md process how does GROMCS know where is the position of the ligand in the complex?


Correspondingly, my second question is, suppose I have a protein dimer with 2 identical subunits, 1 subunit was a cAMP binding, and 1 was apo. Then during the md process how does GROMACS know which subunit binding with the cAMP and which subunit was apo?


I am looking forward to getting a reply from you.


Brett