From AMBER topology to gromacs topology

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ParmEd supports reading and writing to a broad variety of file types, including Amber topology and coordinate files, CHARMM PSF, parameter, topology, and coordinate files, and Tinker parameter, topology, and coordinate files. (Ref: https://github.com/ParmEd/ParmEd)


installing ParmED

1. download from https://github.com/ParmEd/ParmEd.git 

or type this command in the terminal: wget https://github.com/ParmEd/ParmEd/archive/refs/heads/master.zip

2. cd parmedED-master

3. python2.7 setup.py install

4. python setup.py install --prefix=$AMBERHOME

5. source $AMBERHOME/amber.sh

python2.7

>>>import parmed as pmd

>>> amber=pmd.load_file('pro_solv.prmtop', 'pro_solv.inpcrd')

>>> amber.save('prosolv.top')

>>> amber.save('prosolv.gro')

vmd >>> save .trr trajectory file 

OR 

trajout .xtc file in cpptraj



It can also convert various files to other formats such as:

1. convert GROMACS topology to AMBER format

2. convert AMBER topology to GROMACS, CHARMM formats

3. Save a CHARMM PSF and crd files

4. convert mol2 to pdb file



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