Bug #553

pdb2gmx gmx 4.5: issues with atom name in last column

Added by Alan empty over 9 years ago. Updated over 9 years ago.

Erik Lindahl
Target version:
Affected version - extra info:
Affected version:


when using for example:

pdb2gmx -f aQQQ.pdb -o agQQQ.pdb -p -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

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.

aQQQ.pdb (3.86 KB) aQQQ.pdb as requested Alan empty, 09/14/2010 01:07 AM


#1 Updated by David van der Spoel over 9 years ago

Can you please upload the input file?

#2 Updated by Alan empty over 9 years ago

Created an attachment (id=537)
as requested

#3 Updated by David van der Spoel over 9 years ago

Made a patch in commit dfdf261 that fixes this for proteins.

Fixed bug 553 by checking whether an atom name is longer than 2 characters and has a digit in the third character. In that case the name is expected to be protein. However, in this case e.g. Si12 will be designated as Sulphur. The alternative would be to check whether the present residue is an amino acid but that may be problematic as well.

release-4-5-patches and master have been updated.

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