[gmx-developers] Terminal hack blocks do not seem to affect atom mass?

[Berk Hess]

Hi,

This looks mainly like a bug, but could also partially be a feature.
In practice most force fields have atom types with unique masses, so it 
doesn't matter.
But this format currently gives the false impression that you could 
change the mass.

Could you file a redmine issue?

Cheers,

Berk

On 03/21/2013 05:24 PM, Wouter Boomsma wrote:
> Hi,
>
> I'm in the process of implementing a parser for gromacs topology
> files, and have a question about the aminoacids.n.tdb and
> aminoacids.c.tdb type files. In the Gromacs parser, 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. I'm a little uncertain whether this is a
> feature or a bug. Does anyone have any insight in this
> matter?
>
> 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.
>
> Thanks,
> Wouter
>
>
>
>
>

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