votca / csg

Coarse-graining potentials from atomistic references made easy

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csg_dump cannot read pdb

junghans opened this issue · comments

From https://groups.google.com/d/msg/votca/ldn3dPtJ9Lg/f0XKIrWDBAAJ

$ csg_dump --top viton4_10_20_pcff_1.data.mapx.new_v5.pdb
an error occurred:
Misformated pdb file in atom line # 0
 the correct pdb file format requires 80 characters in width. Furthermore,
 to read the topology in from a .pdb file the following attributes must be
 specified:
 Atom Name, Residue Name, Residue Number, x, y, z, charge (optional)

With viton4_10_20_pcff_1.data.mapx.new_v5.pdb

Apparently we read the atomtype from the wrong column, see: https://groups.google.com/d/msg/votca/ldn3dPtJ9Lg/ahMJdqElBQAJ

@JensWehner can you have a look at this?

@junghans does this need to be fixed in development of stable?

I would fix it in stable if possible.