AMBER Archive (2006)

Subject: Re: AMBER: water prmtop/inpcrd problem

From: David A. Case (
Date: Thu Oct 05 2006 - 21:01:22 CDT

On Thu, Oct 05, 2006, Akshay Patny wrote:
> I used LEAP to load this water_mod2.pdb file and then saved
> it as PRMTOP (mod2.prmtop) and INPCRD (mod2.inpcrd) as well
> as PDB (mod2.pdb). Now, when I open the PRMTOP/INPCRD files
> using VMD, there is an extra bond between two hydrogens for
> each water molecule.

This is correct: TIP3P water is a rigid object, and this is implemented in
Amber by having an extra bond between the water hydrogens. If your only
objection is how it "looks" in VMD, you could either mentally ignore it, or
write a VMD script to remove all of those extra bonds. If these extra bonds
are causing some other problem, let us know. There are ways to remove them,
but you have to understand what you are doing.


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