[gmx-users] MD of ligand-only system

vicolls at fizyka.umk.pl vicolls at fizyka.umk.pl
Fri Apr 5 10:49:25 CEST 2019

I want to make MD simulation on retinal molecule in all trans  
conformation. I found the structure in pubchem, downloaded 3d sdf,  
then created mol2 and put this molecule to swiss param server. I get  
bunch of files (pdb, itp etc.). Now I want to use gromacs to make  
simulation. But as far as I've seen simulation  for only one ligand  
(Without protein, without water) should have diffrent commands.  
pdb2gmx doesn't work for example. Where to start with this?

As I said - I've got pdb file and also itp file for charmm ff.

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