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

[Wouter Boomsma]

Hi Berk,

Thanks for your reply. I've filed a redmine issue.

Cheers,
Wouter

On Fri, Mar 22, 2013 at 12:28 PM, Berk Hess <hess at kth.se> wrote:

>  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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-- 
Wouter Boomsma
Postdoc
Structural Biology and NMR Laboratory (SBINLAB)
Department of Biology
University of Copenhagen
Ole Maaløes Vej 5
DK-2200 Copenhagen N, Denmark
E-mail: wb at bio.ku.dk
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