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Converting from amber format into GROMACS

About this tutorial

Ambertools is a freely distributed program for preparing molecular dynamics simulations. If you build your system using Ambertools, then you can convert the Amber topology and coordinate files to GROMACS format using the ACPYE code https://github.com/alanwilter/acpype.

This tutorial will go through the steps of converting an Amber topology and coordinate file into GROMACS format. In this example, we assume you have two files generated from Ambertools:

system_solv.prmtop  -  Amber topology
system_solv.inpcrd  -  Amber coordinate file

The necessary files to run this tutorial can be found here.

Convert amber topology and structure file to GROMACS topology and structure file using ACPYPE

Make sure acpype is in your path and type:

acpype -p system_solv.prmtop -x system_solv.inpcrd -b system_solv

Running this command will produce two files:

system_solv_GMX.top  -  GROMACS topology
system_solv_GMX.gro  -  GROMACS coordinate file

Fix names for Amber14FF

If your system was prepared using Amber14FF, some atom-specific names are not recognized by acpype, so we need to modify the topology file:

sed 's/ 2C / CT /g' system_solv_GMX.top | sed 's/ 3C / CT /g' | sed 's/ IP / Na+/' | sed 's/ IM / Cl-/' > system_solv_GMX_corr.top  

Reorder ions.

Finally, if you added Na+ and Cl- ions in Amber, these can be in a random order in the system_solv_GMX.gro file. Check your .gro file to see if Na+ and Cl- are out of order. GROMACS needs Na+ and Cl- to all be grouped together in the coordinate file. If you need to reorder the ions, you can use the script, reorder.py:

python reorder.py -i system_solv_GMX.gro -o system_solve_GMX_reorder.gro

Now you have a GROMACS topology and coordinate file that can be used to run MD simulations in GROMACS.