AMBER Archive (2009)

Subject: Re: [AMBER] a layer of water

From: oguz gurbulak (
Date: Wed Apr 01 2009 - 02:26:46 CDT

*Packmol (***>
*) was written to generate starting configurations for molecular dynamics.
So you can generate a pdb file for your system using packmol and load it
into xleap. But I think you should look over the manual before you generate
the system. And After you load the packmol pdb file, you must define the box
size in xleap. For example set unit box{ a b c }. *


2009/4/1 Nancy <>

> Dear all,
> I am using amber10, i want to solvate my solute(carbon nanotubes ),i just
> want to solvate the solute in the nozzle of it ,not water surrounding the
> solute. I have tried solvatecap ,but it is not periodic,so can any body tell
> me how to add a layer of water in the nozzle of the carbon nanotubes for
> periodic simulation? Thanks in advance.
> Nancy
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