AMBER Archive (2001)

Subject: Re: adding water

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Oct 13 2001 - 23:44:47 CDT

        I was wondering how I can check the box of water that I am using for my
        simulation( if itfits my protein or not)! I want to make sure that I am
        not using too much of water or vise versa.

You could look at it in xleap or some other visualization program.

        How can I figure out how many water atoms have been added?
        
If you have a pdb file, you can count various things by such
commands as

  % egrep thing file.pdb | wc -l

(count lines with 'thing')

  % egrep thing1 file.pdb | egrep thing2 | wc -l

(count lines with 'thing1' and 'thing2')

  % egrep thing1 file.pdb | egrep -v thing2 | wc -l

(count lines with 'thing1' but not 'thing2')

A look at how water is in your pdb file should suggest a strategy.

Bill Ross