On Fri, Mar 06, 2009, Andrew Voronkov wrote:
> I've tried to rewrite this PDB file by use of Chimera, DS visualizaer
> or Gold-Hermes software, but these programms give the same PDB
> result.
Your coordinates are not in the correct columns in the pdb file.
Compare the top few lines in the LIG file:
ATOM 1 C1 LIG 1 -11.531 -4.269 17.640
ATOM 2 C2 LIG 1 -12.760 -4.099 18.149
ATOM 3 C3 LIG 1 -13.317 -5.417 18.529
ATOM 4 N4 LIG 1 -12.434 -6.371 18.252
with those in sustiva.pdb (which is correct):
ATOM 1 C1 SUS 1 0.728 1.403 0.255
ATOM 2 H1 SUS 1 -0.136 1.756 0.782
ATOM 3 C2 SUS 1 0.803 0.080 -0.150
ATOM 4 C3 SUS 1 -0.290 -0.932 0.158
You will need to have everything in the correct column for your pdb file
to be properly interpreted. Also, you have dos line endings in the
"LIG" file--not sure what antechamber might be doing with those.
...dac
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Received on Sun Mar 08 2009 - 01:11:46 PST
