Dear Amber users,
in some of viewers like Chimera or Discovery Visualizer chlorines from Amber looks like are reconginzed as carbons.
Is it common situation?
Thise parts of PDB which I have got from inpcrd and prmtop using ambpdb are kind of recognized as kind of carbons in some viewers and I became a bit
worried if parametrization for chlorine was ok.
ATOM 3371 H9 RES 211 15.739 47.762 18.647 1.00 0.00 H
ATOM 3372 C17 RES 211 15.396 48.434 16.617 1.00 0.00 C
ATOM 3373 Cl1 RES 211 15.775 50.075 17.009 1.00 0.00 Cl
TER
ATOM 3374 Cl- Cl- 212 -12.953 37.769 28.407 1.00 0.00 Cl
TER
ATOM 3375 Cl- Cl- 213 4.047 59.769 -3.593 1.00 0.00 Cl
TER
This record is recognized as chlorine, but not in Amber:
ATOM 3373 CL1 RES 211 15.775 50.075 17.009 1.00 0.00 CL
Best regards,
Andrew
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Received on Tue Nov 29 2011 - 12:00:06 PST
