AMBER Archive (2002)

Subject: create new atom problem on xleap

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Thu Jul 04 2002 - 15:04:01 CDT

Dear AMBER users:
  I used xleap(AMBER6) to prepare my input prmtop & inpcrd file,
  and the source file(DNA) was taken from PDB(NMR method).
  In case of some problem caused by PROTONATE, I manually replaced
  some atom name(like *to', etc.), and addPdbResMap to define the 4
  Caps on both DNA strands which are end in hydrogen(H3T and H5T),
  addPdbResMap {
  { 0 "CN" "DCN" } { 1 "CN" "DCN" }
  { 0 "GN" "DGN" } { 1 "GN" "DGN" }
  }

  However, xleap still add P groups(P, O1P, O2P) on both 3'
  How can I get such DNA(no P on 5' & 3') without xleap adding P groups?
  Thanks for your help.

  Best Regards,
  sychen