AMBER Archive (2002)

Subject: minimization to fix up hydrogen positions

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Wed May 29 2002 - 02:33:23 CDT

Hi, all,
I'm confused with running minimization to fix up hydrogen positions of
free DNA(the coordinate was taken from its DNA-complex PDB file).

1st, turn on IBELLY(specify H atoms to be moved) or
     Restrain the DNA heavy atoms will be a good idea?
     I've run both of them, but don't know which on is correct.

2nd, How large does 'force constant' should be set in a reasonable range?
     (In tutorial, it is 5000 Kcal/mol)

3rd, What 'atom type' of H or DNA heavy atoms have to be set in
     GROUP Specification? All or just some specific atoms of DNA?

Thank you

Best Regards,
sychen