[gmx-users] MD of ligand-only system

Dallas Warren dallas.warren at monash.edu
Mon Apr 8 23:51:57 CEST 2019

Since you already have the .itp and .pdb then you simply construct your
simulation box, run the energy minimisation etc steps then your production
run.  From the point at which you are currently, of having the topology and
coordinate file, it is the same as for any other simulation (including
protein, protein and ligand, ligand etc).

For general details, including links to tutorials, see

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a

On Fri, 5 Apr 2019 at 19:49, <vicolls at fizyka.umk.pl> wrote:

> 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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