AMBER Archive (2008)

Subject: Re: AMBER: regarding rigid molecules

From: Gustavo Seabra (
Date: Thu Oct 16 2008 - 08:34:56 CDT

On Thu, Oct 16, 2008 at 5:34 AM, aneesh cna wrote:
> Dear Amber Users,
> I am using Amber 9.0 for simulating a system with 3-site
> Carbon dioxide. I want to keep Carbon dioxide as rigid molecules through
> out the simulation. How to do this in Amber? How to mention this in the
> input file ?

Just another option that wasn't mentioned yet... In principle (I
haven't tried it) you could use the "belly" keyword. With it, you cen
define a mask with the atoms you allow to *move*, in the "bellymask".
So, for example if the CO2 is residue 1 on a parmtop file with 300
residues, a bellymask like ":2-300" should do it. But again, I haven't
tried it myself, so I'm not 100% sure it would work.

Good luck,
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