Re: AMBER: Using TIP4P water in free energy calculation

From: David A. Case <>
Date: Thu, 5 Aug 2004 15:35:22 -0700

On Thu, Aug 05, 2004, Lijiang Yang wrote:

> First, I solvated LEU using TIP4P water and saved a perturbation
> topology file. But during my testing, I found that the bonds of LEU residue
> disappeared in md simulation (by looking at the trajactory in VMD).

Can you explain what you mean by "the bonds disappeared"? Did the atoms fly

You can use rdparm to get a list of the bonds in your system. Since the
problem occurs with clambda=0, it has something to do with the unperturbed
Hamiltonian. Your description sounds OK; you may need to post your prmtop
file if you can't figure out anything using rdparm.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Thu Aug 05 2004 - 23:53:01 PDT
Custom Search