AMBER Archive (2003)

Subject: CYS and HIS

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Wed Apr 16 2003 - 09:20:40 CDT

Hi,
  My protein contains a disulfide bond and a HIS is involved in the
ligand binding. I renamed the corresponding CYS and HIS to CYX and HIE
in the pdb file and then loadpdb into xleap and saved the prmtop and
inpcrd files. S-S disulfide bond existed in inpcrd file. After energy
minimization, S-S bond broke up and the distance is over 3 A in the
min.restrt file. It seems to me that loadpdb treats CYS as a residue
name but not the real CYS (including S-S bond). Am I Rright? what is the
normal procedure to deal with CYX and HIE(D/P)?
 I have questions here:
 For CYS, even I changed the res. name, I still need to use BOND to make
the bond in leap and loadpdbusingseq, Or loadpdb will treat CYX as the
defined CYX by AMBER?
 For HIS, after I changed the name to HIE, when loaded into leap, it is
treated as HIE or still the default HIS? Do I need to change the leaprc
file?
 I am an AMBER beginner, If I ask some silly and simple questions,
please don't feel mad at me.
 Thanks a lot.
  Youyi Peng