[gmx-users] PRODRG warning

[Andrew Horsfield]

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