[gmx-users] PRODRG warning

[Daan van Aalten]

Hi Andrew

One problem may be that your PDB file does not have proper atom names.
How can GMX know which "C" is "C" if they are all called "C"? You might
try it with C1 C2 C3 C4 etc. and see if that helps?

cheers

Daan 




On Wed, 16 Jan 2002, Andrew Horsfield wrote:

> Hi Daan,
> 
> Thank you for your e-mail.
> 
> > It might be useful to tell us what ligand you tried to put in, and
> > most importantly what forcefield you trie dto use it with.
> 
> The molecule is pterin. The pdb file is attached at the end of this
> e-mail. I use the ffgmx force field that comes with Gromacs 3.0.5.
> 
> > It has been mentioned pretty explicitly everywhere that *ONLY* the
> > "old" ffgmx forcefield will work.
> 
> What is meant by old here? Is there a Gromacs version number this refers
> to?
> 
> > Other people's tests seem (as far as I am aware) to indicate that GMX
> > topologies straight out of PRODRG seem to work reasonably well,
> > although there appears to be some confusion regarding kJ/kcal units.
> > So send me your ligand, and I'd be happy to look at it.
> 
> (See above).
> 
> Cheers,
> 
> Andrew
> 
> 
> The original pterin.pdb file
> ----------------------------
> 
> ATOM      1  C   UNK     1       0.387  -0.377   0.643  1.00  0.00
> ATOM      2  N   UNK     1      -0.913  -0.533   1.049  1.00  0.00
> ATOM      3  C   UNK     1      -1.841  -0.012   0.290  1.00  0.00
> ATOM      4  N   UNK     1      -1.585   0.663  -0.881  1.00  0.00
> ATOM      5  C   UNK     1      -0.290   0.878  -1.418  1.00  0.00
> ATOM      6  C   UNK     1       0.758   0.284  -0.565  1.00  0.00
> ATOM      7  N   UNK     1       2.034   0.402  -0.962  1.00  0.00
> ATOM      8  C   UNK     1       2.952  -0.128  -0.159  1.00  0.00
> ATOM      9  C   UNK     1       2.598  -0.767   1.044  1.00  0.00
> ATOM     10  N   UNK     1       1.341  -0.900   1.451  1.00  0.00
> ATOM     11  N   UNK     1      -3.152  -0.085   0.684  1.00  0.00
> ATOM     12  H   UNK     1      -3.299  -0.703   1.477  1.00  0.00
> ATOM     13  H   UNK     1      -3.874  -0.120  -0.029  1.00  0.00
> ATOM     14  H   UNK     1      -2.335   1.124  -1.395  1.00  0.00
> ATOM     15  O   UNK     1      -0.150   1.500  -2.458  1.00  0.00
> ATOM     16  H   UNK     1       3.996  -0.040  -0.466  1.00  0.00
> ATOM     17  H   UNK     1       3.370  -1.186   1.695  1.00  0.00
> 


##############################################################################
 
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!
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     C-C-O       O   C-C-C         O             programs/prodrg/prodrg.html
       "         
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