Re: [AMBER] Remove single water molecule using thermodynamic integration

From: <>
Date: Fri, 8 Jan 2016 08:39:39 +0000

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 []
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


AMBER mailing list

AMBER mailing list
Received on Fri Jan 08 2016 - 01:00:03 PST
Custom Search