FAQ DMD

Issues and Questions for DMD

1. I got a state file error when setting up my DMD job.

This is a 'catch-all' error for DMD that can stem from multiple different places. Check the dmd.err file for the full output, but note that this is not easy to understand what the main error is. The first is the substrate. Check to make sure that you do not have any O2, OH, or O oxygens in your system. The error is typically can't assign fftype for atom O.3. DMD does not know how to treat these atoms, and the only known way to run the simulation is to actually treat them as water molecules. Generally, there can also be issues with your substrate where DMD does not know how to handle it. Unfortunately, there is not a lot to do since we do not have a good way of providing non-standard force field terms to DMD for these unusual molecules.

Some times the error is derived from nuclear clashes. Check to see if any atoms are overlapping in your system as well as try deleting the C and N terminus residues. For whatever reason this can fix a lot of issues with DMD, without any real good reason as to why.

Your input pdb could also be missing some heavy atoms. This is fairly typical in crystal structures due to the experimentalists being unable to resolve certain atomic positions. Unfortunately, you have to check the dmd.err file to see which residue this would be and use Chimera (or something similar) to replace those missing atoms. A swapaa change will typically work just fine for these instances.

2. I got an atom labeling error when setting up my DMD job.

Typically this caused by inconsistent labeling of hydrogen atoms within the pdb file. Since DMD will replace all of your hydrogen atoms when it begins the simulation, it is easiest to just delete all of the hydrogens from the file. The heavy atoms will have their standard names being read normally.