AMBER Archive (2009)

Subject: Re: [AMBER] suggestions pls

From: Jio M (
Date: Wed Aug 12 2009 - 08:04:16 CDT

Dear Ashish and Amber Users ,

Thanks for the reply

1) but you didnt mention regarding the method I used to give
environment of residue + water as a solvent to solute. Is this correct
way to provide environment of residue + water to  solute. I have
run the dynamics it was successfull with no error, but I am not
confident for my procedure.

also ---(may be a silly thought)--->

2) is there a way to slowly remove the water while running MD at low
temperature that is  removing water only from the system keeping
solute and residues  at last.  this can be considered
as  "vacuum drying of a system at low temperature (say 10'C)"


solute +n1Water +n2Residues -------Dynamics-Run-(at low temp.)-->> solute + n2Residues

Thanks ,



if my solute variable is "solt" and variable for solvent molecule is
"solv" and both saved in abc.lib

source leaprc.gaff (also loading the frcmod files of solv and solt)

loadoff abc.lib

solvateoct  solt solv 8.0 {this adds solv residues to solt }

loadoff solvents.lib

solvateoct solt TIP3PBOX 8.0

edit solt {this shows water and solv environment around solt}

firstly is this a correct method to follow, if yes then does it
guarantees that TIP3P water is uniformily ditributed ?

It guarantees proper incorporation of TIP3PBOX. What you wanna infer
from uniformly distributed. Are you Planning to define the box and
making the solvent distributed uniformly in the box with application
of boundary parameters for temperature or pressure.


Ashish Runthala,
Faculty Division III,
Assistant Lecturer, Biological Sciences,
Birla Institute of Technology and Science,
Pilani, Rajasthan- 333031

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