[gmx-users] N terminus charge groups in ffG53a6

[David van der Spoel]

van Bemmelen wrote:
> 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?
> 
Good point. Please submit a bugzilla.

-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se