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pdb2gmxThis program reads a coordinate file, typically a PDB file, reads some database files, adds hydrogens to the molecules and generates coordinates in .gro format (by default) and a topology in .top format. These files can subsequently be processed by grompp to generate a run input file, tpr. Note that a PDB file is nothing more than a file format, and it need not necessarily contain a protein structure. Every kind of molecule for which there is support in the database can be converted, but if it is not there it will fail with an error. If there is no support in the database, you can add it yourself. The pdb2gmx program is typically used for large molecules that have repeating units or residues, such as proteins, DNA and polymers; it makes generation of the topology file easier / faster. UseIf you want to use pdb2gmx to automatically generate your topology, you have to ensure that the appropriate .rtp entry is present within the desired force field and has the same name as the building block you are trying to use. If you call your molecule "HIS," then pdb2gmx will not magically build a random molecule; it will try to build histidine, based on the If you want a topology for an arbitrary molecule, you can not use pdb2gmx (unless you build the .rtp entry yourself). You will have to build it by hand, or use another program to build the .top file.
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