From: Kshatresh Dutta Dubey (
Date: Tue Dec 09 2014 - 09:39:10 CST

Dear Users,

  I have amber generated trajectories and I am willing to take some
snapshots for QM/MM calculation using chemshell that runs fine with charmm
psf and pdb file. But the different nomenclature of hydrogen for charmm and
amber is creating the problem from direct use of amber generated pdbs. Is
it correct if I save the coordinates without H and then re-adding them in
psfgen and going further for QM/MM calculations? Please suggest me about
the appropriateness of this method.