[gmx-users] MD simulation of ligand only system

vicolls at fizyka.umk.pl vicolls at fizyka.umk.pl
Fri Apr 5 11:41:26 CEST 2019

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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