Re: [AMBER] bond connections

From: Jason Swails <>
Date: Thu, 3 Dec 2015 07:41:11 -0500

On Thu, Dec 3, 2015 at 2:02 AM, mohammad r <> wrote:

> Hi everybody,
> As I am new to the amber, I want to know that when I’mgenerating my
> system, is it necessary to define all the bonds between atoms andmolecule?
> Actually my system is consisted of a protein and some lipids(whichthe pdb
> file is generated by packmol) and then it is solvated in water
> (inambertools) and neutralizing the system(by addionsrand command). I just
> definethe forcefield and libraries for protein, water and lipids then load
> the pdbfile and solvated it in water and finally save the topology and
> coordinatefiles. But when I start running the MD I think the bonds are
> messed. There issomething wrong with the internal bonded interactions.

​Without more details of what you did, it's impossible to determine what
may have gone wrong.

Use VMD to visualize your topology and coordinate files that you get from
Amber. Do the bonds look OK there? VMD draws bonds according to what is
defined in the topology file, so visualizing what VMD tells you the bonds
are is a good way to determine whether or not your prmtop is missing bonds.

tleap/xleap add bonds according to the residue templates -- so if the
residue template says there is a bond between two atoms with a specific
name, then leap will add a bond between those two atoms from the PDB file.
There's no intelligence or chemical intuition built into leap -- it does
exactly what you tell it to.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Dec 03 2015 - 05:00:05 PST
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