[gmx-users] molecule of metane

[Justin A. Lemkul]

This is a common error that has been discussed numerous times on this list
(hint: check the archives).  pdb2gmx is not magic, so also check out:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

With a name like MET, pdb2gmx is expecting methionine, not methane.

-Justin

Quoting Foh <foh at uni.udm.ru>:

> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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