Just read the code! :-)
[Chris is the original author of leap.]
On 9/15/16 5:57 PM, Christian Schafmeister wrote:
> Howdy,
>
> I’m loading a PDB file for a large DNA/protein complex.
> The DNA residues look like what I’ve attached below.
> It contains atom names like C1*, C2*, C3*, C4* for the ribose carbons.
> The nucleic acids in files like amber/dat/leap/lib/nucleic10.lib label their ribose carbons as C1’, C2’, C3’, C4’
>
> (1) Are these ribose atoms equivalent? Was there a change in how ribose atoms are named?
> or
> (2) Do I have the wrong residue files and I need to use residue files with ribose carbons named C1*, C2*, C3*, C4* ?
>
> ATOM 27829 C2* DC L 50 94.816 120.688 -57.522 -0.0854 1.700
> ATOM 27827 C3* DC L 50 94.667 120.189 -58.958 0.0713 1.700
> ATOM 27825 C2 DC L 50 97.029 119.538 -54.813 0.7959 1.700
> ATOM 27824 N3 DC L 50 97.633 120.025 -53.698 -0.7748 1.550
> ATOM 27821 N4 DC L 50 98.468 121.760 -52.466 -0.9773 1.550
> ATOM 27820 C4 DC L 50 97.877 121.335 -53.572 0.8439 1.700
> ATOM 27818 C5 DC L 50 97.515 122.267 -54.597 -0.5222 1.700
> ATOM 27816 C6 DC L 50 96.912 121.760 -55.703 -0.0183 1.700
> ATOM 27815 N1 DC L 50 96.670 120.428 -55.820 -0.0339 1.550
> ATOM 27813 C1* DC L 50 96.009 119.872 -57.034 -0.0116 1.700
> ATOM 27810 C4* DC L 50 96.118 119.935 -59.366 0.1629 1.700
> ATOM 27807 C5* DC L 50 96.726 120.979 -60.281 -0.0069 1.700
> ATOM 27799 C2* DT L 51 91.299 117.211 -55.918 -0.0854 1.700
> ATOM 27797 C3* DT L 51 91.279 116.032 -56.888 0.0713 1.700
> ATOM 27795 C2 DT L 51 93.736 118.109 -53.339 0.5677 1.700
> ATOM 27793 N3 DT L 51 94.187 119.268 -52.738 -0.4340 1.550
> ATOM 27791 C4 DT L 51 94.115 120.543 -53.259 0.5194 1.700
> ATOM 27787 C7 DT L 51 93.378 121.961 -55.205 -0.2269 1.700
> ATOM 27786 C5 DT L 51 93.498 120.611 -54.564 0.0025 1.700
> ATOM 27784 C6 DT L 51 93.051 119.500 -55.171 -0.2209 1.700
> ATOM 27783 N1 DT L 51 93.164 118.271 -54.577 -0.0239 1.550
> ATOM 27781 C1* DT L 51 92.665 117.044 -55.259 0.0680 1.700
> ATOM 27778 C4* DT L 51 92.744 115.933 -57.312 0.1629 1.700
> ATOM 27775 C5* DT L 51 93.056 116.469 -58.693 -0.0069 1.700
> ATOM 27767 C2* DT L 52 88.812 114.359 -52.353 -0.0854 1.700
> ATOM 27765 C3* DT L 52 89.094 112.878 -52.606 0.0713 1.700
> ATOM 27763 C2 DT L 52 90.943 116.957 -50.905 0.5677 1.700
> ATOM 27761 N3 DT L 52 91.081 118.327 -51.018 -0.4340 1.550
> ATOM 27759 C4 DT L 52 90.678 119.105 -52.083 0.5194 1.700
> ATOM 27755 C7 DT L 52 89.590 119.132 -54.354 -0.2269 1.700
> ATOM 27754 C5 DT L 52 90.058 118.362 -53.155 0.0025 1.700
> ATOM 27752 C6 DT L 52 89.912 117.029 -53.071 -0.2209 1.700
> ATOM 27751 N1 DT L 52 90.343 116.335 -51.973 -0.0239 1.550
> ATOM 27749 C1* DT L 52 90.176 114.857 -51.889 0.0680 1.700
> ATOM 27746 C4* DT L 52 90.532 112.905 -53.122 0.1629 1.700
> ATOM 27743 C5* DT L 52 90.689 112.717 -54.616 -0.0069 1.700
>
> Christian Schafmeister
> Professor, Chemistry Department
> Temple University
> meister.temple.edu
>
>
>
>
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Received on Fri Sep 16 2016 - 13:30:02 PDT
