[gmx-developers] pdb2gmx and water, git version 4.0.99_development_20090605

[Berk Hess]

Hi,

Ah, this is a bug due to the residue number retaining that I introduced.
I fixed it in git.

Berk

Michel Cuendet wrote:
>
> Hi all,
>
> Berk : Thanks for your reply to my previous post. Sorry I didn't have
> time to re-check on the latest git. You might also have fixed this one
> already...
>
> Again, this works fine with 4.0.4.
>
> I am now trying to pass a box of water through pdb2gmx. To make things
> as simple as possible, I reproduce the error with one water only in a
> pdb file :
>
> TITLE test
> ATOM      1   OW HOH      1      12.002  18.332  13.055  1.00  0.00
> ATOM      2  HW1 HOH      1      12.792  18.711  12.671  1.00  0.00
> ATOM      3  HW2 HOH      1      11.702  17.694  12.406  1.00  0.00
> END
>
> echo 2 | pdb2gmx -f one_water.pdb
>
> [ ... some ouput ... ]
> Moved all the water blocks to the end
> There are 0 chains and 2 blocks of water and 0 residues with 3 atoms
>
>  chain  #res #atoms
>  1 '-'     1      1  (only water)
>  2 '-'     1      2  (only water)
>
> WARNING: there were 0 atoms with zero occupancy and 2 atoms with
>         occupancy unequal to one (out of 3 atoms). Check your pdb file.
>
> [ ... some ouput ... ]
>
> WARNING: atom OW is missing in residue HOH 0 in the pdb file
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.99_development_20090605
> Source code file: pdb2top.c, line: 771
>
> Fatal error:
> There were 1 missing atoms in molecule Water, if you want to use this
> incomplete topology anyhow, use the option -missing
> For more information and tips for trouble shooting please check the
> GROMACS Wiki at
> http://wiki.gromacs.org/index.php/Errors
> -------------------------------------------------------
>
> Cheers,
> Michel
>