[gmx-users] pdb2gmx gmx 4.5: issues with atom name in last column

Alan alanwilter at gmail.com
Thu Sep 9 18:37:09 CEST 2010

Hi there,

when using for example:

pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p agQQQ.top -ff amber99sb -water none

I got in the agQQQ.pdb, things like:

ATOM     15  NE2 NGL     1       4.309   7.159   2.648  1.00  0.00
ATOM     16 1HE2 NGL     1       4.030   7.698   3.448  1.00  0.00
ATOM     17 2HE2 NGL     1       5.066   7.449   2.048  1.00  0.00
ATOM     18  C   NGL     1       5.487   2.636   0.037  1.00  0.00

Notice the last column, in special the "HE". This is wrong!

For most programmes it's not a issue since they seem to ignore the last
column but this column exist and has a propose.

And there programmes that observe this column, like openbabel. If converting
this pdb to mol2 I got wrong structure since babel thinks I am dealing with
Helium atoms.

In gmx 4.0.x the last column was never printed so never had this problem



Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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