[gmx-users] MD simulation of ligand only system

[Dallas Warren]

http://manual.gromacs.org/documentation/current/user-guide/run-time-errors.html#invalid-order-for-directive-xxx

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
nail.


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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