AMBER Archive (2002)

Subject: Re: Molecular dynamic protocol...

From: David A. Case (case_at_scripps.edu)
Date: Fri Dec 27 2002 - 13:25:51 CST

On Fri, Dec 27, 2002, Andrei Leitão wrote:
>
>
> There are no errors in the prmtop file, but the output
> archive shows the following message in the :
> ...
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> &wt
>
> It appears that the comand &wt is not correct. Here is my
> file (this is very similar to the DNA tutorial one):

As the manual indicates (p. 106), section TWO (weight change information)
is only read if nmropt>0, but you have left it at the default value of
zero.

Hence, the program is expecting to see the group information where you
have the weight change information, and it thinks "&wt" is the title of
the group information section.

You need to set nmropt=1 in your input file if you want to use weight change
information. If you don't have any nmr restraints, create a dummy file,
and add the command

DISANG=dummy

after your weight change information, but before the group information.

[TEC: we *really* need to replace the group information section of sander...]

..hope this helps...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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