A force field is not something that is magical, it can only deal with molecules or residues (building blocks) that are provided in the residue database or included otherwise. A residue database entry may be missing simply because the database does not contain the residue at all, or because the name is different.įor new users, this error appears because they are running pdb2gmx blindly on a PDB file they have without consideration of the contents of the file. This entry defines the atom types, connectivity, bonded and non-bonded interaction types for the residue and is necessary to use pdb2gmx to build a. formaldehyde) or a peptide (standard or non-standard). The residue database entry is necessary both for stand-alone molecules (e.g. This means that the force field you have selected while running pdb2gmx does not have an entry in the residue database for XXX. Residue 'XXX' not found in residue topology database If it takes a long time, have a think about what you are doing, and the underlying algorithm (see the manual, man page, or use the -h flag for the utility), and see if there's something sensible you can do that has better scaling properties. The user should bear in mind that the cost in time and/or memory for various activities will scale with the number of atoms/groups/residues N or the simulation length T as order N, Nlog N, or N 2 (or maybe worse!) and the same for T, depending on the type of activity. in some cases confusion between Ångström and nm may lead to users wanting to generate a water box that is 10 3 times larger than what they think it is (e.g.reduce the length of trajectory file being processed.reduce the scope of the number of atoms selected for analysis.The executed script has attempted to assign memory to be used in the calculation, but is unable to due to insufficient memory. There is no domain decomposition for n nodes that is compatible with the given box and a minimum cell size of x nm
#There is not enough memory to open zero k needed software#
Software inconsistency error: Some interactions seem to be assigned multiple times A charge group moved too far between two domain decomposition steps. X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group Can not do Conjugate Gradients with constraints Converged to machine precision, but not to the requested precision Stepsize too small, or no change in energy. Invalid line in coordinate file for atom X The sum of the two largest charge group radii (X) is larger than rlist - rvdw/rcoulomb
The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. T-Coupling group XXX has fewer than 10% of the atoms Number of coordinates in coordinate file does not match topology Atom index n in position_restraints out of bounds No force fields found (files with name 'p' in subdirectories ending on '.ff') Atom X in residue YYY not found in rtp entry WARNING: atom X is missing in residue XXX Y in the pdb file
Chain identifier 'X' was used in two non-sequential blocks
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