Re: [AMBER] Particle insertion and deletion

From: Carlos Simmerling <>
Date: Sun, 14 Mar 2010 17:06:51 -0400

see below

On Sun, Mar 14, 2010 at 4:14 PM, Dian Jiao <> wrote:

> Hello,
> 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?
you don't need a prmtop for each frame, just 1 new prmtop with the original
system as well as teh new particle.
you do need to write a program that will place the prarticle to insert.
Amber doesn't know how to do that.

> 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
> bondtype.....properly".
> Does anyone know a better way to handle this?\

probably a better was is to modify the prmtop to make the parameters for
this atom equal to zero. (charges, vdw etc). this may not always be easy to
do. you might need to use antechamber to make the new residue with the
particle there, but edit it to give it new parameters and then include it in
your prmtop.

you could also modify the code to ignore the energies for this particle.

in general, Amber is not set up to do such calculations easily. maybe others
will have suggestions.

> Thanks in advance.
> ~Dian
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Received on Sun Mar 14 2010 - 14:30:02 PDT
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