Re: [AMBER] TImask command for PMEMD

From: David A Case <>
Date: Mon, 2 Oct 2017 17:26:26 -0400

On Mon, Oct 02, 2017, Roma Mukhopadhyay wrote:
> When we run TI for explicit models, do we have to consider the water
> residues also in the 'timask' ? If I have residues of interest from
> 1-3, and water from 7-731 for one molecule and for the other molecule
> I have residues 4-6, and water from 732-1456 in my pdb file then how
> should I put in my TI mask. I have tried doing " timask1=':1-3 :7-731',
> timask2=':4-6 :732-1456',"

Note that the mask specifies which atoms/residues are being changed, not
which parts of the molecule are "of interest". It would be rather rare to
mutate a water molecule into something else. You would certainly never mutate
hundreds of residues at a time.

> timask1=':1-3, :7-731', timask2=':4-6, :732-1456'

Remove spaces from the masks. (But also remove the residues that are waters.)


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Received on Mon Oct 02 2017 - 14:30:03 PDT
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