Na ion in amber99sb.ff/ions.itp

[Nobuyuki MATUBAYASI]

When reading  amber99sb.ff/ions.itp and extracting the information about the Na ion, the MolPrm file reads

  1 N 1 0.71128 0.325

The LJ parameters in it actually correspond to nitrogen.

This may be cause due to the procedure

  atype = ls[1].upper()

in the 225th line (in 0.3.rc1) in gromacs/gen_structure;

Na is then converted to NA, with which the nitrogen parameters are subsequently assigned.

For the moment, user needs to modify his/her MolPrm file manually

[Nobuyuki MATUBAYASI]

This point is now [ermod:tickets] #36.

2015年5月8日金曜日 13時02分33秒 UTC+9 Nobuyuki MATUBAYASI: