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

[David van der Spoel]

On 2010-09-09 18.37, Alan wrote:
> 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
>      N
> ATOM     16 1HE2 NGL     1       4.030   7.698   3.448  1.00  0.00
>     HE
> ATOM     17 2HE2 NGL     1       5.066   7.449   2.048  1.00  0.00
>     HE
> ATOM     18  C   NGL     1       5.487   2.636   0.037  1.00  0.00
>      C
>
I can not reproduce this. Can you please file a bugzilla and load up the 
input pdb file?


> 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
> before.
>
> Thanks,
>
> Alan
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>  >>http://www.bio.cam.ac.uk/~awd28<<
>


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se