Re: [AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask

From: xueqin pang <pangxueqintea.yahoo.com.cn>
Date: Fri, 26 Nov 2010 16:41:42 +0800 (CST)

Hi Jason,

     Thanks for reply. Actually I searched both  restraint and 10 (which is my restraint_wt), but find nothing, that is why I ask. Attached is the out put, can you check it for me.

     Many thanks for your kind help

Best wishes

Xueqin

--- 10年11月25日,周四, Jason Swails <jason.swails.gmail.com> 写道:

发件人: Jason Swails <jason.swails.gmail.com>
主题: Re: [AMBER] where to check output restraint-wt (ntr=1) decleared with restraintmask
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年11月25日,周四,下午11:54

At some point during the output file, it prints out all of the potential
parameters.  The value of restraint_wt is printed there.

Good luck!
Jason

On Thu, Nov 25, 2010 at 9:52 AM, xueqin pang <pangxueqintea.yahoo.com.cn>wrote:

> Hello everyone,
>
>       I am using Amber11 to do MD simulation. In order to restraint heavy
> atoms only I set the restraint with "  restraint_wt  = 10.0,  restraintmask
> = "(:1-206 | :359-607) & !.H=" " instead of GROUP.
>       So where to check the   restraint_wt  in the output. I get only
> following related information in the output. So how can we can the
> restraint_wt or it is simply because I have not restraint the molecular at
> all?
>
>    5.  REFERENCE ATOM COORDINATES
>       Mask (:1-206 | :359-607) & !.H=; matches  1865 atoms
>      EAMBER (non-restraint)  =   -122185.0850
>
>      As for the GROUP restraint, amber will give an output as follow:
>
>     ----- READING GROUP     1; TITLE:
>  Hold the protein
> fixed
>      GROUP    1 HAS HARMONIC CONSTRAINTS    10.00000
>  GRP    1 RES    1 TO   200
>       Number of atoms in this group  =  3253
>     ----- END OF GROUP READ -----
>
> Thanks very much with your kind help
>
> Best wishes
>
> Xueqin
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
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 Fri Nov 26 2010 - 01:00:03 PST
Custom Search