[gmx-users] PRODRG warning

[Daan van Aalten]

Dear GMXers

As to the PRODRG problem reported this morning, the version that is now on
the server is now correct, and tested with Andrew Horsfield's problem
molecule.
Please let me know if any of you experience further problems.

cheers

Daan


On Wed, 16 Jan 2002, Andrew Horsfield wrote:

> Hi David,
> 
> > Furthermore the output force constants are in kcal and Angstrom rather 
> > than kJ and nm.
> 
> I replied too quickly a moment ago. The bond data from PRODRG is:
> 
>    1   2   1 0.100       895.0 ;    HA    N
>    2   3   1 0.140       800.0 ;     N    C
>    2  12   1 0.140       800.0 ;     N    C
>    3   4   1 0.123      1200.0 ;     C    O
>    3   5   1 0.139      1000.0 ;     C    C
>    5   6   1 0.134      1000.0 ;     C    N
>    5  10   1 0.139      1000.0 ;     C    C
>    6   7   1 0.132      1000.0 ;     N    C
>    7   8   1 0.139      1000.0 ;     C    C
>    8   9   1 0.132      1000.0 ;     C    N
>    9  10   1 0.134      1000.0 ;     N    C
>   10  11   1 0.134      1000.0 ;     C    N
>   11  12   1 0.134      1000.0 ;     N    C
>   12  13   1 0.133       900.0 ;     C    N
>   13  14   1 0.100       895.0 ;     N   HC
>   13  15   1 0.100       895.0 ;     N   HB
> 
> The bond lengths are clearly in nm. I cannot determine the units of the 
> spring constants from here by eye.
> 
> Cheers,
> 
> Andrew
> 
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##############################################################################
 
Dr. Daan van Aalten                    Wellcome Trust RCD Fellow 
Wellcome Trust Biocentre, Dow Street   TEL: ++ 44 1382 344979 
Div. of Biol.Chem. & Mol.Microbiology  FAX: ++ 44 1382 345764 
School of Life Sciences                E-mail: dava at davapc1.bioch.dundee.ac.uk
Univ. of Dundee, Dundee DD1 5EH, UK    WWW: http://davapc1.bioch.dundee.ac.uk 

        O     C           O     C         Visit the PRODRG server to take 
        "     |           "     |         the stress out of your topologies!
  N--c--C--N--C--C--N--C--C--N--C--C--O   
     |           "     |           "      http://davapc1.bioch.dundee.ac.uk/
     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
       O