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
Received on Thu Jul 04 2002 - 13:04:01 PDT
