[gmx-users] MD simulation of ligand only system

Dallas Warren dallas.warren at monash.edu
Mon Apr 8 23:54:47 CEST 2019


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 20:41, <vicolls at fizyka.umk.pl> wrote:

> I want to make MD simulation on retinal molecule in all trans
> conformation. No protein, no water at all,  just pure retinal. 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.). I used editconf to generate gro  from pdb.
> Now I want to use gromacs to make energy minimization. But when I try
> grompp I get Fatal error:
> Syntax error - File ret_all_trans.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes
> I thought that swiss-param will generate ready to go files. But it
> seems it's not. What should I  do next?
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