[gmx-users] perfluorohexane pdb... again
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Mon Jan 10 21:17:45 CET 2011
Hi Justin
As i have said in the message the pdb file needs probably some (small) changes. emacs (or vi) and vmd or rasmol are our friends ;)
Below the pdb file in the correct format (tested with rasmol and vmd)
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011
ATOM 1 C1 HEF 0 -11.336 -0.581 0.212 1.00 0.00 C
ATOM 2 C2 HEF 0 -10.035 -0.174 -0.542 1.00 0.00 C
ATOM 3 C3 HEF 0 -8.771 -0.197 0.410 1.00 0.00 C
ATOM 4 C4 HEF 0 -7.458 0.219 -0.369 1.00 0.00 C
ATOM 5 C5 HEF 0 -6.194 0.196 0.583 1.00 0.00 C
ATOM 6 C6 HEF 0 -4.893 0.603 -0.171 1.00 0.00 C
ATOM 7 F7 HEF 0 -11.590 0.293 1.248 1.00 0.00 F
ATOM 8 F8 HEF 0 -11.226 -1.862 0.712 1.00 0.00 F
ATOM 9 F9 HEF 0 -12.391 -0.539 -0.675 1.00 0.00 F
ATOM 10 F10 HEF 0 -10.216 1.097 -1.046 1.00 0.00 F
ATOM 11 F11 HEF 0 -9.852 -1.059 -1.582 1.00 0.00 F
ATOM 12 F12 HEF 0 -8.977 0.685 1.449 1.00 0.00 F
ATOM 13 F13 HEF 0 -8.613 -1.470 0.913 1.00 0.00 F
ATOM 14 F14 HEF 0 -7.617 1.493 -0.871 1.00 0.00 F
ATOM 15 F15 HEF 0 -7.252 -0.663 -1.408 1.00 0.00 F
ATOM 16 F16 HEF 0 -6.377 1.082 1.623 1.00 0.00 F
ATOM 17 F17 HEF 0 -6.013 -1.074 1.087 1.00 0.00 F
ATOM 18 F18 HEF 0 -5.004 1.884 -0.671 1.00 0.00 F
ATOM 19 F19 HEF 0 -4.639 -0.271 -1.207 1.00 0.00 F
ATOM 20 F20 HEF 0 -3.839 0.561 0.716 1.00 0.00 F
END
Stephane
> Re hi Marcelo,
>
> Below the perfluorohexane molecule in the pdb format construct with
> the Discovery Studio Visualizer v2.5
>
> REMARK Accelrys Discovery Studio PDB file
> REMARK Created: Mon Jan 10 20:52:13 Paris, Madrid 2011
> HETATM 1 C1 0 -11.336 -0.581 0.212 1.00 0.00
> C
> HETATM 2 C2 0 -10.035 -0.174 -0.542 1.00 0.00
> C
> HETATM 3 C3 0 -8.771 -0.197 0.410 1.00 0.00
> C
> HETATM 4 C4 0 -7.458 0.219 -0.369 1.00 0.00
> C
> HETATM 5 C5 0 -6.194 0.196 0.583 1.00 0.00
> C
> HETATM 6 C6 0 -4.893 0.603 -0.171 1.00 0.00
> C
> HETATM 7 F7 0 -11.590 0.293 1.248 1.00 0.00
> F
> HETATM 8 F8 0 -11.226 -1.862 0.712 1.00 0.00
> F
> HETATM 9 F9 0 -12.391 -0.539 -0.675 1.00 0.00
> F
> HETATM 10 F10 0 -10.216 1.097 -1.046 1.00 0.00
> F
> HETATM 11 F11 0 -9.852 -1.059 -1.582 1.00 0.00
> F
> HETATM 12 F12 0 -8.977 0.685 1.449 1.00 0.00
> F
> HETATM 13 F13 0 -8.613 -1.470 0.913 1.00 0.00
> F
> HETATM 14 F14 0 -7.617 1.493 -0.871 1.00 0.00
> F
> HETATM 15 F15 0 -7.252 -0.663 -1.408 1.00 0.00
> F
> HETATM 16 F16 0 -6.377 1.082 1.623 1.00 0.00
> F
> HETATM 17 F17 0 -6.013 -1.074 1.087 1.00 0.00
> F
> HETATM 18 F18 0 -5.004 1.884 -0.671 1.00 0.00
> F
> HETATM 19 F19 0 -4.639 -0.271 -1.207 1.00 0.00
> F
> HETATM 20 F20 0 -3.839 0.561 0.716 1.00 0.00
> F
> END
>
> The structure needs some changes (atom names ?) and minimization
> steps to relax the structure.
>
If you want Gromacs to read this file, it also needs residue names.
PDB format is fixed, and this set of coordinates is not correctly
formatted, so it will undoubtedly cause problems in Gromacs.
-Justin
> hope this helps
>
> Stephane
>
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