AMBER Archive (2002)

Subject: Re: create new atom problem on xleap

From: Bill Ross (photoriot_at_yahoo.com)
Date: Thu Jul 04 2002 - 15:58:59 CDT

> ... 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" }
> }
> ...
> ...How can I get such DNA(no P on 5' & 3')
> without xleap adding P groups?

The correct terminal nucleic acid residues can
be found by inspecting the existing leaprc's,
e.g. for G:

  { 0 "G" "DG5" } { 1 "G" "DG3" }

Therefore in this case:

  { 0 "GN" "DG5" } { 1 "GN" "DG3" }

Bill Ross

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