AMBER Archive (2009)

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

From: Wei Zhang (zgjzweig_at_gmail.com)
Date: Mon Apr 06 2009 - 07:57:21 CDT

On Apr 6, 2009, at 7:52 AM, Tomasio, Susana wrote:

> 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!)

Look for command: solvateBox 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
>>
>>
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