CHARMM topology question
Hi,
I want to add bonds, angles and dihedrals to my structure. It has some missing atoms, but I don't want them there on purpose. When I create the topology, those atoms are automatically added to the structure. Is there a way to tell it not to add any missing atoms?
I use the following code:
IMP::atom::CHARMMParameters* ff = new IMP::atom::CHARMMParameters(topology_file_name, parameter_file_name); IMP::atom::CHARMMTopology* topology = ff->create_topology(mhd_); topology->setup_hierarchy(mhd_); IMP::ParticlesTemp bonds = topology->add_bonds(mhd_); IMP::ParticlesTemp angles = ff->create_angles(bonds); IMP::ParticlesTemp dihedrals = ff->create_dihedrals(bonds);
Thanks! Dina
On 8/15/12 11:57 AM, Dina Schneidman wrote: > I want to add bonds, angles and dihedrals to my structure. It has some > missing atoms, but I don't want them there on purpose. > When I create the topology, those atoms are automatically added to the > structure. > Is there a way to tell it not to add any missing atoms?
When in doubt, read the documentation. ;)
> topology->setup_hierarchy(mhd_);
This is for the common use case "tidy up the hierarchy so it matches the topology, by adding/removing atoms as necessary". If you don't want to do that, call the functions it calls yourself, leaving out add_missing_atoms().
Ben
I guess I should just read the code :) Thanks!
On Fri, Aug 17, 2012 at 11:07 AM, Ben Webb ben@salilab.org wrote: > On 8/15/12 11:57 AM, Dina Schneidman wrote: >> >> I want to add bonds, angles and dihedrals to my structure. It has some >> missing atoms, but I don't want them there on purpose. >> When I create the topology, those atoms are automatically added to the >> structure. >> Is there a way to tell it not to add any missing atoms? > > > When in doubt, read the documentation. ;) > >> topology->setup_hierarchy(mhd_); > > > This is for the common use case "tidy up the hierarchy so it matches the > topology, by adding/removing atoms as necessary". If you don't want to do > that, call the functions it calls yourself, leaving out add_missing_atoms(). > > Ben > -- > ben@salilab.org http://salilab.org/~ben/ > "It is a capital mistake to theorize before one has data." > - Sir Arthur Conan Doyle > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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Ben Webb -
Dina Schneidman