Re: [AMBER] questions about Amber to run MD of Amoeba

From: m13654940810 <>
Date: Mon, 22 Sep 2014 20:45:19 +0800

Dear Jason

Thank you very much for your help.




发件人:Jason Swails <>
发送时间:2014-09-22 20:36
主题:Re: [AMBER] questions about Amber to run MD of Amoeba

On Mon, 2014-09-22 at 20:12 +0800, m13654940810 wrote:
> Hi,
> Here is my mdin file:
> minimize
> &cntrl
> imin=1,maxcyc=3000,ncyc=1000,
> cut=10.0,
> iamoeba=1,
> ntpr=500,
> ntr=1,
> restraintmask=':1-20',
> ntb=1,
> restraint_wt=100.0
> /
> &amoeba
> /
> the systerm is about DNA.
> the message in the mdout file is:
> Spline order too small. Must be at least 5.

The B-spline interpolation order is, by default, 4. The Amoeba force
field requires a B-spline order of at least 5. So you need to add an
&ewald section to your input file and set order=5:


We should probably make 5 the default for Amoeba simulations...

> Another question : Can I just use tleap to prepare the solvent box of
> DNA with TIP3PBOX(the systerm is perpared for amoeba force field),if
> not ,what should I do ?

Yes, that should be fine. In fact, this strategy is recommended on page
276 of the Amber 14 manual. I recommend perusing that part of the
manual for advice here.


Jason M. Swails
Rutgers University
Postdoctoral Researcher

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Received on Mon Sep 22 2014 - 06:00:05 PDT
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