AMBER Archive (2003)

Subject: Re: AMBER: GIBBS - PMF problem: Lambda has not changed

From: Jiri Matousek (matousek_at_chemi.muni.cz)
Date: Thu Nov 13 2003 - 11:09:49 CST

Hi David,
firstly thak you for answer. I tryied to correct my input file in the
way which you have suggested. Nothihg has changed, gibout file and
MICSTAT file are similar as before. Pleas be so kind and look on my
problem one more.

Thank you...

Jiri

David Smith wrote:
> Hi Jiri,
>
> A quick look through your input options seems to indicate to me that
> everything looks OK (except 11 windows of 100 steps each won't give you
> a very useful result :)
>
> I think the problem is with the formatting of the constraints section.
> If I try to quickly line up yours with one of mine:
>
>
> 14 41 0 0 0 0 2 0.00000 1.00000
> 100.00000 5.40000 100.00000 10.40000 0 0
>
> 06595 11954 00000 00000 00000 00000 00002 000.00000 001.00000
> 0000.00000 008.00000 000.00000 038.41020 0000 0000
>
>
> then I notice that "RLAMDA2" field is not quite in the right place. The
> second line is also offset a bit. This could be due to the way it is in
> the mail etc so I would suggest that you look near the beginning of the
> gibout file. For my example above the section looks like:
>
>
> READING INTERNAL RESTRAINTS/CONSTRAINTS:
> ----------------------------------------
>
> SG ( 6595)-S48 ( 11954) :
> IUMB=0 IZE=0 ITOR=2 IPER= 0 IPER2= 0 LAM1= 0.000 LAM2= 1.000
> K1= 0.0000 Req1= 8.0000 K2= 0.0000 Req2= 38.4102
>
>
> This way you can check if what you think these variables should be is
> the same as what the program thinks.
>
> If this is not the problem then just post again and I (or maybe someone
> else) will have a closer look.
>
> Good luck...
>
> David.
>
>

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