Extra atoms not removed from pdb file
The attached PDB file has an N-terminal PRO with two hydrogens names H2 & H3.
pdb2gmx (correctly) assigns an NH2+-terminus, but then goes ahead and adds H1 - without removing H3.
The end result is that there is one hydrogen too much, and incorrect (non-integer charge).
This is apparently present in 4.0.7 too.
#2 Updated by Erik Lindahl about 9 years ago
Fixed by commit 11e839e7ea1828b2233894ba9ff2d8202263cd2f.
There was some old code lying around that made an exception for N-terminal hydrogens, but since these are now properly added in the RTP I see no reason why we should not apply the same rule for those.