[gmx-developers] Terminal hack blocks do not seem to affect atom mass?
hess at kth.se
Fri Mar 22 12:28:28 CET 2013
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
But this format currently gives the false impression that you could
change the mass.
Could you file a redmine issue?
On 03/21/2013 05:24 PM, Wouter Boomsma wrote:
> 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 ]
> 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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