[gmx-users] pdb2gmx gmx 4.5: issues with atom name in last column
David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 9 21:57:13 CEST 2010
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
> 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
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
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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
More information about the gromacs.org_gmx-users