AMBER Archive (2008)

Subject: Re: AMBER: anion and cation simulaton

From: FyD (
Date: Tue Mar 25 2008 - 14:54:56 CDT

Quoting gurpreet singh <>:

> I am using amber 9 for an anion (PF6) and equal number of cation
> simulation. After some steps, some of P-F bonds were not visible when seen
> in softwares like VMD.

If you load your prmtop file and then a restrt file from your MD
simulation in VMD as a _single_ molecule you should see the correct
connectivities (all the bonds). If not, this means your initial
topology is wrong. A simple way to check that could be to generate a
Tripos mol2 file of your initial structure and visualize it in VMD
(See to generate a
Tripos mol2 file from a prep or OFF library in LEaP). If it does not
contain the correct number of bonds, there is something wrong in the
way you generated your initial libraries for your PF6 anion...

regards, Francois

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