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

[Michel Cuendet]

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

-- 

==========================================================
Michel Cuendet, Ph.D
Molecular Modelling Group
Swiss Institute of Bioinformatics
CH-1015 Lausanne, Switzerland
http://lausanne.isb-sib.ch/~mcuendet
==========================================================