AMBER Archive (2003)

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

From: David Smith (David.Smith_at_cup.uni-muenchen.de)
Date: Thu Nov 13 2003 - 08:00:48 CST

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. 

-- 
---------------------------------------
Dr. David Smith
Department of Chemistry
Ludwig Maximilians University
Butenandt-Str. 5-13, D-81377 Munich
Germany
Tel.: +49 (0)89 2180 77740
Fax.: +49 (0)89 2180 77738
e-mail: David.Smith_at_cup.uni-muenchen.de
---------------------------------------

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