Re: [AMBER] simulation with glycans

From: Sundar <>
Date: Wed, 16 Jan 2019 09:14:33 -0600

As far as I know, charmm-gui generates Amber files to directly start you
simulations in Amber.
Why are you using 'chamber'? Are you trying to convert charrmm files to
If yes, you don't have to if you get Amber files straight from charmm-gui.


On Wed, Jan 16, 2019 at 4:48 AM Jacopo Sgrignani <> wrote:

> Dear all
> could anybody help me to understand how to run a simulation with pmemd
> generating the input file with this charmm tool (
> for a protein that include glycans.
> I generated some files with glycan reader and modeller, and I thought to
> convert these using chamber. However, I'm not sure about which are the
> files to convert or if I have to use these to produce other files (with
> water for example) and then convert these new files with chamber.
> thanks in advance
> Jacopo
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Sundar Thangapandian
AMBER mailing list
Received on Wed Jan 16 2019 - 07:30:03 PST
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