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

Wouter Boomsma wb at bio.ku.dk
Thu Mar 21 17:24:07 CET 2013


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

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    =

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.

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