GROMACS version:2020.2
GROMACS modification: No
Hello dear all!
I am trying to simulate a mixture of testosterone propionate - benzene. When I start grompp an error appears:
Syntax error - File BEN.itp, line 1
Last line read:
‘[defaults]’
Topologies and coordinates received using LigParGen.
In the .itp files I made a full explicit description and put them in the oplsaa.ff folder. In the .top file, i left only links to .itp and [system] [molecules]
Moreover, if you run only benzene, everything starts successfully.
What could be the reason?
Files .itp .top attached.
Thank you in advance!)
Benzene(BEN.itp) and testosterone propionate(TP.itp);
[ defaults ]
…
[ atomtypes ]
…
[ moleculetype ]
…
[ atoms ]
…
[ bonds ]
…
[ angles ]
…
[ dihedrals ]
…
[ dihedrals ]
…
[ pairs ]
…
topol.top;
#include “oplsaa.ff/TP.itp”
#include “oplsaa.ff/BEN.itp”
[ system ]
Testosterone propionate - Benzene!
[ molecules ]
UNK 102
BEN 323
Why do you have [ defaults ] and [ atomtypes ] in the molecule’s .itp file?
Those can only be called once, and are typically found in the FF definition files.
Molecule.itp file
I wrote atomtypes to .itp files because in my oplsaa field there are no atom types from 800 to 899 and LigParGen gave these types to my atoms. Parameters may be incorrect. By the way, is it generally normal that I do not have these types of atoms in oplsaa?
If I have all the parameters set explicitly, then it makes no sense to refer to forcefield.itp and I added [defaults] to the molecule.itp.
That was my train of thought.
I don’t know about the fact that they are called only once. I’ll try a little later.
Thank!
It all depends on what the expectations of the topology generator is. It sounds like LigParGen is giving you a standalone topology for the molecule, such that there are no dependencies on other files. That works fine if all you’re simulating is that molecule alone or in water, etc. but if you have other things going on (multiple small molecules, a biomolecule, etc) you will have to edit the small-molecule topology and/or be judicious with the #include statements that reference it, such that all force-field level directive precede all molecule-level directives.