VMD-L Mailing List

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Sat Aug 12 2006 - 18:52:49 CDT

Hi,

On Sat, Aug 12, 2006 at 06:45:17PM -0500, sseefeld_at_uwm.edu wrote:
> I should be doing pdb alias residue HOH TP3M not TIP3 because the TIP3 is
> setting up the H1 H2 bond. Where as the TP3M is just the two O-H bonds. This
> makes my earlier modification to the parameter file useless. I'm going to try
> this quick and then reply again.

Just for the records, the solvate plugin in VMD uses modified version of
TIP3, which doesn't contain the H-H bond. So, even though it uses the
residue name TIP3, it's actually the same as TP3M.

Of course, this does not apply if you use waters that we're not placed
by solvate, as I assume is your case.

Best,
Leo 

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign