MATCH Server

FAQ

What will I receive as output

A topology file (.rtf) which contains the atom types, charges and bonding connectivity, a parameter file (.prm) containing all the bond, angle, dihedral angles, improper angles and non bonded parameters for the molecule. Finally a pdb of the given molecule will also be included that is in charmm compatible format making it easy to load in the coordinates in a charmm script.

Is there any specific type of file format that works best?

Generally supplying the connectivity for a molecule works the best such as in (.mol, mol2 and .sdf) but the pdb parser is very good and works in a high percentage of the time. If you are having issues getting MATCH to read a file please consult the user guide which outlines the expected format for each file format.

How do I load these files into CHARMM? are there examples?

Sure are! You can either look in the user guide that you can download, or you can download this example that minimizes a molecule if you supply the name of the directory it exists in.

Known errors and possible solutions

____ has too many bonds for its element, structure is warped

The atom mentioned has been predicted to bond to too many atoms, this is most likely an error in MATCH's ability to parse a pdb or the actual structure have atoms that are too close together making them appear to be bonded. One can supply the correct bonding using a MOL/MOL2/ SDF file.

Could Not Type Atom With State

It is not possible to type this atom, first thing to check is the atom state reported. Which is in the format Atom Element . Number of bonds. If either the atom element is wrong or the number of bonds is wrong that is the likely reason why typing failed. The atom element being wrong is rather rare something CL atoms are mistaken as C due to the atom name. If the number of bonds is wrong then follow a similar procedure as the following error. If both are correct then it is most likely that the forcefield does not cover the given chemical environment. Where there is not much that can be done.

The increment between atoms () and () does not exist and Increment Substitution failed to yield an acceptable result

First check the types which are the atoms are assigned as they are within the parentheses next to the atom information. Investigating whether the atom type makes sense for the given chemical environment is the first step in debugging this error. It is highly suggested you download the package to try and debug this issue. If the types are okay then most likely there is not much that can be done other than to manually assign the increment by looking at the existing increments of the .incr file of the force field of interest.