Prmtop file

Worst case, you'll just get garbage results. It's always easier to debug on a small number of processors and a small number of frames. Once you have that working, then you should scale up. Reading command-line arguments and input files This format is supported by VMD beginning with version 1.

It is also available as a PDF. Force field parameter file specification. Last modified: May 3, Codes that write prmtop files need to ensure that the values entered in this section satisfy the rule given above; similarly, codes that read prmtop files need to interpret these values in the same way that Amber does. This is, after all, an "Amber" file format! Gromacs and some other programs currently [] use a conversion factor of Conversions to or from the prmtop format may need to take account of such small differences, if they are important.

See ICO below. Also called IBLO. All possible or atoms type interactions are represented. NOTE: A particular atom type can have either a or a interaction, but not both. It is inverted right after it's read in for performance reasons. This allows variable scaling. If not present, it defaults to 1. It is inverted right after it's read in. If not present, it defaults to 2.

Indexed like CN1 above. Index into these arrays is equivalent to the CN1 and CN2 arrays, however the index is negative. Indexed like ASOL. For most users, simply ensuring that at least one of the above packages is available and working and using the default will suffice. For the other small percentage that may want more fine-grained control, the use function will let you specify a particular implementation to use.

You can change the back-end at any time, but note that the behavior of a NetCDF object created with one implementation is undefined if you switch to a different one. The character : is used for residue selections and is used for atom selections.

Both numbers and names are supported in the atom and residue selections where the serial numbers range from 1 to N , where N is either the total number of atoms or residues, depending on what is being selected. Examples of residue selections, accompanied by comments annotating what is being selected, is shown below:. You can select all residues that are a specific element if you want to. Examples are shown below, accompanied by comments annotating what is being selected:.

Be careful, though! These element names are case-sensitive, and bad element names will cause the mask parser to raise an exception. In some cases, it is more succinct to select by atom type name, rather than atom name. Be careful though! Atom type names can change from force field to force field, and are considered an implementation detail. You have been warned. Note, no indices or index ranges can be used, as atom types have no defined order.

Examples are shown below:. You often want to select certain atoms from certain residues. This is so common, you can use a simple shortcut, demonstrated below, giving equivalent expressions to the examples above:.

You can also expand your selection using the or operator. The above example selects all atoms if it satisfies the criteria of being in the first residues or if it satisfies the criteria of having the name CA , meaning it selects all atoms in the first residues and all atoms named CA.

Sometimes you also want to be able to select all atoms within a certain distance or all atoms within a residue that is a certain distance from a specific set of atoms.

This is probably the most complex part of the Amber mask syntax, but it is also quite powerful. When selecting residues, the whole residue is selected if any atom satisfies the distance criteria. Examples are shown below with annotations:. Core classes used to represent topologies The core Structure class Working with units Reading and writing files The Amber file classes The parameter-topology prmtop file parmed.

AmberFormat parmed. AmberParm parmed. ChamberParm parmed. AmoebaParm parmed. Create a free Team What is Teams? Collectives on Stack Overflow. Learn more. How to load. Ask Question. Asked 3 years, 11 months ago. Active 3 years, 10 months ago. Viewed times. Universe topology, trajectory I saw this thread and also this library which I don't want to use if I can read Amber.

Improve this question. Is your "amberOut. I am asking because MDAnalysis recognizes files with. If it is a restart file, try passing the explicit format argument to the Universe: Universe See also github.