Dear Users, I have an amber prmtop, and inpcrd file, which I am converting to gromacs top, and gro files using following lines of code:
import parmed as pmd
amber=pmd.load_file(‘complex_solvated.prmtop’,‘complex_solvated.inpcrd’)
amber.save(‘complex_solvated.top’, format=‘gromacs’)
amber.save(‘complex_solvated.gro’)
The saved top file has correctly kept the original atom index, but unfortunately, the gro file has reindexed every atom of the system. I am looking for a keyword to disable the reindexing option, but could not find. I tried reindex=False, atomgroup.reindex=False, but looks like either I am using wrong keyword. Could anyone please help me?
Thanks.