Dear Amber Users,
I would like to remove atoms related to phosphate group in the residue (say
for example tyrosine) in the restart file and add hydrogen to the oxygen
atoms.
I tried using cpptraj and parmed.py using the command
strip :PTR&!(25781-25784) (something like this and atom number 25781 to
25784 corresponds to phosphate group)
However, the command does not remove any atoms and mentioning only PTR
strips the entire residue.
Please advice how to remove the specific atoms in the restart file and save
a new top and rest file.
Many Thanks
Balaji
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Received on Mon Feb 22 2016 - 11:00:02 PST
