Re: [AMBER] Replacing water with a H2O2 and restart the simulation

From: David A Case <>
Date: Fri, 27 May 2016 07:51:17 -0400

On Thu, May 26, 2016, Morteza Chehel Amirani wrote:
> I have a simulation which was running for 10 ns. Now, I want to replace one
> of water molecules with a hydrogen peroxidase. I'm wondering what the best
> way is to kind of restart the simulation?
> Do I need to prepare the topology file from the scratch, or I can make a
> new topology file only for the peroxide and combine it with the original
> one?

You can convert your final structure to PDB format, manually change one
water molecule to H2O2, then use loadPdb to bring the modified file into LEaP
and create a new topology file.

> In the case I make the a new topology file for the new system, how can I
> import the simulation box information into it?

Use the set <unit> box command in LEaP to do this. For sanity, check that the
last line of the newly-created rst7 file matches the last line of the final
restart file from the earlier simulation. (If you have unformatted restart
files, which is recommended and is now the default, use cpptraj to convert
to a formatted file, then you can examine the final line.)

...good luck....dac

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Received on Fri May 27 2016 - 05:00:03 PDT
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