Dear Amber supporters,
antechamber sometimes generates different(wrong) atom types and
force field parameters even if we use same molecule structures.
Results with AmberTools12 are as follows:
(molecule 1)
HETATM 1 C 0 -0.858 0.151 0.000
HETATM 2 C 0 0.521 0.151 0.000
HETATM 3 C 0 0.936 1.538 0.000
HETATM 4 C 0 -0.218 2.294 -0.000
HETATM 5 H 0 -1.632 -0.610 -0.000
HETATM 6 H 0 1.186 -0.708 0.000
HETATM 7 H 0 1.962 1.892 -0.000
HETATM 8 H 0 -0.448 3.355 -0.000
HETATM 9 C 0 -1.338 1.461 -0.000
HETATM 10 C 0 -2.636 1.849 -0.005
HETATM 11 H 0 -2.888 2.889 -0.008
HETATM 12 O 0 -3.674 0.865 -0.005
HETATM 13 H 0 -4.529 1.301 -0.007
=>
cc
cd h4
cc c2
cd oh ho
cc
(molecule 2, which is created by shuffling lines of molecule 1)
HETATM 3 C 0 0.936 1.538 0.000
HETATM 9 C 0 -1.338 1.461 -0.000
HETATM 12 O 0 -3.674 0.865 -0.005
HETATM 10 C 0 -2.636 1.849 -0.005
HETATM 8 H 0 -0.448 3.355 -0.000
HETATM 5 H 0 -1.632 -0.610 -0.000
HETATM 7 H 0 1.962 1.892 -0.000
HETATM 2 C 0 0.521 0.151 0.000
HETATM 1 C 0 -0.858 0.151 0.000
HETATM 13 H 0 -4.529 1.301 -0.007
HETATM 4 C 0 -0.218 2.294 -0.000
HETATM 11 H 0 -2.888 2.889 -0.008
HETATM 6 H 0 1.186 -0.708 0.000
=>
cd
cc h4
cd c2
cc oh ho
cd
Would you let me know why this happens?
What should I do for getting right result?
Best regards,
--
Hiromasa WATANABE
Manager, Ph.D.
HPC Dept., Technology Gr., HPC SYSTEMS Inc.
Head office: LOOP-X 8F, 3-9-15 Wangan, Minato-ku, Tokyo, Japan 108-0022.
Email: hi-watanabe.hpc.co.jp
www.hpc.co.jp
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Received on Sun Aug 11 2013 - 20:00:03 PDT
