Thank Jason and Dan.
2014-09-22
m13654940810
发件人：Daniel Roe <daniel.r.roe.gmail.com>
发送时间：2014-09-22 22:06
主题：Re: [AMBER] questions about Amber to run MD of Amoeba
收件人："AMBER Mailing List"<amber.ambermd.org>
抄送：
When you are using Cartesian restraints (ntr = 1), you need to specify
a reference structure on the command line with '-ref'. You should read
the Amber 14 manual (section 17.6.4 in particular) for more details.
-Dan
On Mon, Sep 22, 2014 at 7:28 AM, m13654940810 <m13654940810.163.com> wrote:
> 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
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Sep 22 2014 - 08:00:03 PDT
