pure TIP5P water system with AMBER7 parameters

From: satya work (satya.work_at_gmail.com)
Date: Wed Apr 18 2007 - 11:23:26 CDT

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Dear all,

I am trying to run a pure TIP5P water system using AMBER7 parameters. I have
created 'prmcrd and prmtop' files but I see that early in the simulation the
two lone pairs overlap and I see a continous worm-like structure for water.
My questions are:

1. Has anyone tried running TIP5P water system with AMBER parametes and
faced similar problem?
2. How are dummy particles (like the lone pair in TIP5P) treated in NAMD? As
I understand, *The way in which the "off-atom" points in TIP5P (and similar
models) **are handled in sander is partially hardwired ( From AMBER
archives).
* 3.Has anyone used CHARMM parameters ( if they exist) for TIP5P in NAMD?

Thanks
Vani
*
*

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