Re: [AMBER] Macromolecular crowding force-field and parameters

From: Lijuan Yu <>
Date: Thu, 13 Aug 2015 12:15:55 +0800

Hi Richa,

How are you?

I saw you are using AMBER and I am the beginner of AMBER. Now I can access
AMBER on Raijin. But I don't know how to set the AMBER environment and how
to use AmberTools.

Could you kindly please tell me the steps to set this?

I know I should not sent email to you about Amber stuff. The NCI help guy
Andrey did give me some suggestions. But I still do not know how to set
this up.

Your help is greatly appreciated.

Many Thanks,


On 12 August 2015 at 11:55, richa anand <> wrote:

> Hi,
> I am using AMBER12 package, want to study the Macromolecular Crowding
> effect on RNA-protein complexes. Can any one suggest me what should be the
> applied force-field, simulation parameters and co-ordinates (distance of
> macromolecules from RNA-protein complexes) during simulation?
> Any suggestions would be most helpful.
> Regards,
> Richa Anand
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Received on Wed Aug 12 2015 - 21:30:04 PDT
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