ffld2gmx

Python Script to transform Force Field files from Schrödinger's Maestro (.ffld) to GROMACS (.itp, .top)

How to get your FFLD in Maestro

First, build your geometry in maestro and save the geometry as a .mae file

Second, convert your .mae geometry to .pdb with the following command in terminal:

$SCHRODINGER/utilities/pdbconvert -no_reorder -imae **.mae -opdb **.pdb

Open the generated .pdb file and delete the CONNECT lines. (this step is not mandatory but it can avoid errors)

Third, generate the .ffld topology using the following command:

$SCHRODINGER/utilities/ffld_server -version 14 -print_parameters -ipdb **.pdb > **.ffld

Once you have your topology.ffld topology file, the next step is to use the transformer.

Usage

To use this script one just need to have the ffld2gmx.py script in the same directory as your topology.ffld. The .ffld file will be used as argument for the script:

python ffld2gmx.py topology.ffld

Important: The script also requires to have the file ffnotbonded.itp file in the same directory so it can read the non-bonded parameters from the OPLS-AA force field tailored to GROMACS.

The output of the script are two files:

1. A residue topology file called UNK.itp so one can change the name to the residue name desired.
2. A topology file called topol.top that serve as template for your simulation topology file. The residue topology UNK.itp is automatically linked with the directive: #include "UNK.itp"

Test file

To start checking the usage one can use the test.ffld file included in this repository.

Final disclaimer:

• The automatic force field generated is a OPLS-AA force field. For other force fields one need to use other tools to transform those.
• Transition metals force constants are not reliable and needs to be computed independently.