Dear Amber users:
I remember that sometime ago cpptraj was able to strip atoms from the
prmtop file, but it was suggested that we use that only for visualization
purposes, not for simulations. Is this still the case? Or I can use a
stripped prmtop for simulations?
And in case I can use it for MD, when I strip some residue in a protein, do
I need to first remove the bonds connecting that residue to the others, or
is this done automatically by cpptraj?
Thanks,
Ignacio
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Received on Tue Mar 26 2013 - 07:30:03 PDT
