[AMBER] Particle insertion and deletion

From: Dian Jiao <oscarjiao.gmail.com>
Date: Sun, 14 Mar 2010 14:14:20 -0600


I was trying to analyze the energy by inserting a particle or deleting a
particle from an existing trajectory.

1. Insertion
I have run simulation with a box of water and wanted to insert a particle
with random position and orientation to each frame and reevaluate the
energies. How do I do that? Do I need to generate new trajectory with the
particle and also new prmtop for each frame and analyze it?

2. Deletion
I know how to delete a particle from a trajectory with "STRIP" command. But
again, how to generate new prmtop (w/o the particle) from the old prmtop?
I thought I could do it this way: pick one frame from the simulation
trajectory of a waterbox with the particle and manually remove the particle
from the pdb. Then use antechamber to generate the mol2 and leap to create
prmtop and inpcrd. As it turned out, the antechamber didn't work, couldn't
generate the mol2 for waterbox, because of the "cannot run

Does anyone know a better way to handle this?

Thanks in advance.

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Received on Sun Mar 14 2010 - 13:30:03 PDT
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