Dear Jason,
I modified input file as you said ,and there is another issue :
Unit 10 Error on OPEN: refc
Sorry to trouble you again .
Thanks
2014-09-22
m13654940810
发件人："m13654940810"<m13654940810.163.com>
发送时间：2014-09-22 20:45
主题：Re: [AMBER] questions about Amber to run MD of Amoeba
收件人："AMBER Mailing List"<amber.ambermd.org>
抄送：
Dear Jason
Thank you very much for your help.
Guowei
2014-09-22
m13654940810
发件人：Jason Swails <jason.swails.gmail.com>
发送时间：2014-09-22 20:36
主题：Re: [AMBER] questions about Amber to run MD of Amoeba
收件人："amber"<amber.ambermd.org>
抄送：
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 22 2014 - 06:30:02 PDT
