I want to use cpptraj for some analysis but my topology and trajectory file is in .top and .xtc or .trr format. Please give me resoponse for how to run parmed command in a proper way to convert topology and trajectory files from gromacs to amber.
Hi,
Please check mdconvert, if it will be able to convert the file format.
Hi,
For the topology you can use tleap to create parm file with the same information such as protein, number of water molecule, number of ion, boxtype ..etc.
For the trajectory file, you can write simple code to take the coordinate from gro file, then write it in crd format of AMBER.
If you provide the gromacs files including system.top, initial-system.gro and traj.xtc (just several snapshots for example), I may help you write the code to create the topology and trajectory file to work with cpptraj as you want.
Best,
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