[gmx-users] molecule of metane

Foh foh at uni.udm.ru
Wed Nov 21 15:37:24 CET 2007


Hello

I ask to help.
Now I study program GROMACS.
Has taken for an example file PDB - the molecule of metane:

ATOM 1 CT MET 1 3.875 0.678-8.417 1.00 0.00
ATOM 2 HC MET 1 3.800 1.690-8.076 1.00 0.00
ATOM 3 HC MET 1 4.907 0.410-8.516 1.00 0.00
ATOM 4 HC MET 1 3.406 0.026-7.711 1.00 0.00
ATOM 5 HC MET 1 3.389 0.583-9.366 1.00 0.00
END

Further I create files
methane.gro And methane.top
pdb2gmx-f methane.pdb-p methane.top-o methane.gro-missing
With use OPLS of potential (a position 3 in the program pdb2gmx)
3) oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)

The message, that is deduced
fatal error - I can not find the description of the given atoms in base.

Probably a mistake in the description of structure.
The image of the report I apply.

I work with the version for Windows.

I ask to help.
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