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

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 22 Sep 2014 08:36:29 -0400

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:

&ewald
   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.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 22 2014 - 06:00:03 PDT
Custom Search