Re: [AMBER] free energy calculation: turn off the VDW interaction between ligand and protein

From: case <>
Date: Fri, 30 Dec 2011 20:19:35 -0500

On Sat, Dec 31, 2011, Bing Xiong wrote:
> By reading the manual (amber 10), the softcore part stated that we
> can turn off the charge with crgmask. Can we turn off the vdw interaction of
> ligand with protein as commonly used in double decouping
> calculations? how to do this in amber? such as how to prepare the V1
> state(V0 is the vdw interaction on, charge=0.0 )? is there any parameter
> like crgmask for turn off the VDW interaction?

If I understand your question correctly, the usual way to prepare a "V1"
state where there is no coupling between the ligand and the environment is
simply to leave the ligand out when making the prmtop file. The TI
implementation in sander does not require the same number of atoms in the two
end states.

Please see tutorial A9 for a worked-out example.


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Received on Fri Dec 30 2011 - 17:30:04 PST
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