AMBER Archive (2009)

Subject: RE: [AMBER] Amber with AMOEBA force-field

From: Tomasio, Susana (S.M.T.Tomasio_at_warwick.ac.uk)
Date: Mon Apr 06 2009 - 07:52:01 CDT

Thank you for your reply.

I am trying to run the example in amber10/test/sleap/amoeba, but I don't know how to create and solvate the box in sleap.
(I mean the commands.. can't find it in the manual!)

I have an extension of the amoeba force-field which I would like to use.

Thank you,

Susana

-----Original Message-----
From: amber-bounces_at_ambermd.org on behalf of Wei Zhang
Sent: Mon 4/6/2009 1:48 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Amber with AMOEBA force-field
 
Hi,

    Can you be more specific about the problem with sleap?
I wrote the problem, so I might be able to help.

    Currently, amoeba only has parameters for amino acid.
Thus it will be hard to build system other than protein.

     SIncerely,

     Wei

On Apr 6, 2009, at 7:41 AM, Tomasio, Susana wrote:

>
> Hi all,
>
> I am trying to use amber with the amoeba force-field.
>
> Does anyone have an example/tutorial of see how it works.
>
> I am having problems with the sleap; xleap doesn't seem to work with
> the amoeba force-field.
>
> Thanks in advance,
>
> Susana
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber