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
Received on Sat Oct 13 2001 - 21:44:47 PDT
