Contributors

David Case, T. Meyer

Comments

These are libraries and parameters for the modified bases appearing in tRNA-phe from yeast:

1MA 1-methyl-adenosine
2MG 2-mehtyl-guanosine
M2G dimethyl-guanosine
7MG 7-methyl-guanosine
YG Wybutosine
5MC 5-methyl-cytosine
PSU pseduouridine
5MU 5-methyl-uridine
H2U 5,6-dihydro-uridine
O2C O2'-methyl-cytosine
O2G O2'-methyl-guanosine
SPM spermine
5GP 5'-guanosine

Charges were calculated with the RESP procedure, at the HF/6-31G* level.

Force constants and atom types were hand-assigned, based by analogy to the parm99 force field.

A artificial bond between P and H5T in the 5' guanosine nucleotide was added to prevent distortion of the terminal OH group; this is similar to the artificial H-H bond in water that keeps it rigid.

An accompanying leap script is also available.

These libraries were created by Tim Meyer and David Case. Contact David Case with questions or comments.


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Last modified Wed Apr 23 08:53:33 BST 2003