Re: [AMBER] free energy calculation with TI

From: <>
Date: Wed, 16 Mar 2011 05:25:15 -0400 (EDT)


> V0 and V1 only differ by the solute molecule. Is there a way to generate a
> prmtop file by taking out the solute atoms and keep the all other atoms
> the
> same? Or it has to be done manually?

that is normally no problem when you plan it in advance while building
your system. Say at some point in leap, you have saved your
solute+waterbox as you would for a normal simulation:

> saveamberparm system xxx yyy

then you can remove the solute

> remove system system.1

and save the solutefree waterbox without any changed coordinates

> saveamberparm system xxxV1 yyyV1

Kind Regards,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Mar 16 2011 - 02:30:04 PDT
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