[AMBER] TImask command for PMEMD

From: Roma Mukhopadhyay <roma1988.nmsu.edu>
Date: Mon, 2 Oct 2017 17:01:12 +0000

Hi ,

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',"

 timask1=':1-3, :7-731', timask2=':4-6, :732-1456', but neither seemed to work.

What is the proper syntax for applying TI mask, since there are too many molecules I don't want to use .1,.2,.,3,.7,....731?
 Do I need to use TI merge? If yes, is there a way I could proceed even without using it.

Please let me know how I should proceed.


From: Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk>
Sent: Friday, August 18, 2017 4:36 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Thermodynamic Integration using PMEMD

On Fri, 18 Aug 2017 16:13:46 +0000
Roma Mukhopadhyay <roma1988.nmsu.edu> wrote:

> Then I try to run minimization on it. The ti mask i have applied is
> "timask1=':1',timask2=':2' ". However my output file generates this
> information:

Your two identical molecules are made up of 3 residues each. You can
see that in molx.pdb (BTW, new.leap actually reads two and
writes one, all differently named, PDB files which obviously means
that's not how you have set that up). So, you should have timask =
':1-3', timask2 = ':4-6'.

> Energy averages sample interval:
> | ene_avg_sampling = 1
> TI Mask 1 :1; matches 6 atoms
> TI Mask 2 :2; matches 13 atoms

Here you see how many atoms you have in those two residues.

> TI region 1: 37 atoms
> TI region 2: 44 atoms

Add these numbers to the numbers above and you will have your total of
50 atoms.

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Received on Mon Oct 02 2017 - 10:30:02 PDT
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