Thank you for your fast answer!
Joe
On 01/08/2016 09:39 AM, hannes.loeffler.stfc.ac.uk wrote:
> This is probably one of the technically simplest transformations you can carry out with AMBER. What you want to do is to decouple your water molecule, that is scale all non-bonded interactions between your water molecule and the environment while preserving the internal bonded and non-bonded (water doesn't have any) interactions. All you need to do is to set both ti/scmask1 to the water molecule in question and ti/scmask2 will both be an empty string.
>
> ________________________________________
> From: Johannes Loeffler [johannes.r.loeffler.gmail.com]
> Sent: 08 January 2016 08:10
> To: AMBER Mailing List
> Subject: [AMBER] Remove single water molecule using thermodynamic integration
>
> Dear all,
>
> I am currently trying to remove a single water molecule from a binding
> pocket using thermodynamic integration. Is a transformation to nothing
> somehow possible or do i need to transform water to dummy atoms? (either
> pmemd or sander)
>
> Thank you in advance
>
> Joe
>
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Received on Fri Jan 08 2016 - 01:00:04 PST
