[gmx-users] N terminus charge groups in ffG53a6

[van Bemmelen]

Hi guys,

I have a question about the assignment of charge groups at the
N-terminus when applying the GROMOS 53a6 force field. But this may also
be relevant to other force fields.

When I run pdb2gmx (gmx 3.3.1) on a protein (lysozyme 1AKI in this
case), it gives the following N terminus topology:
==========
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1         NL      1   LYSH      N      1      0.129    14.0067
     2          H      1   LYSH     H1      1      0.248      1.008
     3          H      1   LYSH     H2      1      0.248      1.008
     4          H      1   LYSH     H3      1      0.248      1.008
     5        CH1      1   LYSH     CA      2      0.127     13.019
     6        CH2      1   LYSH     CB      2          0     14.027
[...]
==========
In this way, cg1 has a total charge of +0.873 and cg2 has a total charge
of +0.127.

Moreover, when I select an NH2 terminus with the -ter option, the
topology becomes:
==========
;   nr       type  resnr residue  atom   cgnr     charge       mass
     1         NL      1   LYSH      N      1      -0.66    14.0067
     2          H      1   LYSH     H1      1       0.44      1.008
     3          H      1   LYSH     H2      1       0.44      1.008
     4        CH1      1   LYSH     CA      2      -0.22     13.019
     5        CH2      1   LYSH     CB      2          0     14.027
[...]
==========
Now cg1 has a total charge of +0.22 and cg2 exactly the opposite.

Of course this is only a minor detail. But wouldn't it be better and
more consistent if the CA atom would be assigned to cg1 instead of cg2,
in both cases?

Cheers,
Jeroen