hello guys. I am trying to get into MD, however i am struggling to go beyond the tutorials that are already around. there is this tutorial:
http://www.mdtutorials.com/gmx/
which describes a ligand-receptor complex. however, what if i have multiple ligands? i can just keep adding them to the topology, but then how do i constrain them?
thank you in advance
I have never seen such a tutorial. I’m not a specialist with proteins. My guess is that one would try to test binding with and without the cofactor present. But better you have a look into literature and find papers where people simulate protein + ligand + cofactor.
The approach is the same, the only modification would be that if both non-standard entities require the introduction of new parameters or atom types, those have to be collated into a single file before any molecule topology can be #included in the system .top file. All force field parameters have to be known before any molecule can be defined.
thank you for the reply! i managed to get it running like that. i put the ligand atoms into an atoms.itp, that i included before the molecule types and that allowed me to run it just fine!