AMBER Archive (2009)

Subject: Re: [AMBER] suggestions pls

From: Ashish Runthala (ashish.runthala_at_gmail.com)
Date: Tue Aug 11 2009 - 21:40:40 CDT

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 ?

See
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 

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

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