AMBER Archive (2008)

Subject: Re: AMBER: Help with NMODE

From: Seth Lilavivat (sethl_at_gatech.edu)
Date: Mon May 05 2008 - 14:39:06 CDT

On Sun, May 4, 2008 at 9:26 PM, David A. Case <case_at_scripps.edu> wrote:

> On Sun, May 04, 2008, Seth Lilavivat wrote:
>
> > The results that I am reporting are after I set scee = 1.2
>
> Are the two results excactly 20% different? Are you sure that you
> "setting"
> of scee=1.2 is being recognized by the program? Posting actual inputs and
> outputs would help: take the same starting structure and run one step of
> minimzation in both programs.
>

It looks like mm_pbsa.pl is creating a correct nmode.in file. However, when
I look at the nmode.out file, apparently not all of the parameters are being
read in correctly as you suggested. Interestingly, scee = 1.2 but the maxcyc
and the diel are not changed from default. I've been scratching my head and
trying to figure out how this is possible.

>
>
> Also, I don't recall getting the answer to the question of what version of
> Amber you are using (maybe I missed it). I ask because the error messages
> you
> are reporting don't seem to correpond to the codes I have looked at.
>

I am running AMBER 8

Cheers,
Seth

>
> ...dac
>
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