GROMACS

In aminoacids.n.tdb and aminoacids.c.tdb type files
it seems that when specifying a rule like this:

[ NH3+ ]
[ replace ]
N N NH3 14.0027 -0.3
CA CA CT1 12.011 0.21
HA HA HB 1.008 0.10
[ Add ]
3 4 H N CA C
HC 1.008 0.33 -1
[ delete ]
HN

The mass specification - for instance the 14.0027, is not
used in the generation of the topology file, in contrast to
the charge value. It is not completely clear that this is
really a bug, but it is surprising behaviour that masses
in the hack blocks are ignored.

Code wise, the responsible lines are in the pdb2top.c file,
in the name2type function:

at->atom[i].type = restp[resind].atom[j].type;
            at->atom[i].q    = restp[resind].atom[j].q;
            at->atom[i].m    = get_atomtype_massA(restp[resind].atom[j].type,
                                                  atype);

At this point in the code restp[resind].atom[j].m actually
contains the modified mass, but this is not copied to the
"at" object, which is later written to the topology file.