[gmx-developers] Re: xlate_atomname_gmx2pdb in pdbio.c

Jian Zou jianzou at gmail.com
Mon Oct 27 22:06:52 CET 2008

Hi David,

Thank you so much for the explanation. You are right, the first two
columns in the name field should be the element name.

Anyway, vmd works well for both formats (H5'1 or 1H5') and I will
change my script according to the gmx4 setup.


David van der Spoel wrote:
> To adhere to the pdb standard. You can not have characters in the left
> most column, since they will be interpreted as elements. For instance
> HG11 (leucine side chain) would turn this atom into a Mercury atom. If
> you rename it as 1HG1, it is clear.
> Of course your example is different. I am not sure there is a perfect
> solution though.

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