[gmx-users] no residue type with Amber99SB-ILDN ff

[Mark Abraham]

On Fri, Feb 6, 2015 at 12:43 PM, Ahmet yıldırım <ahmedo047 at gmail.com> wrote:

> Dear users,
>
> I get the following error when i use pdb2gmx tool of GROMACS 4.6.5, with
> the AMBER99SB-ILDN ff. My command:
> pdb2gmx -f protein.pdb -o protein.gro -p protein.top
>
> Fatal error:
> In the chosen force field there is no residue type for 'LYS' as a
> standalone (starting & ending) residue
>
> The pdb2gmx gives this error though terminal residues are prefixed with N
> and C.
>

Maybe those prefixes are in the wrong columns of your input .pdb file.


> Could there be something wrong with the input .pdb file? But i dont get
> this error with another forcefield, 43a2.
>

GROMOS force fields handle termini differently from AMBER, so that's
expected.

Mark


>
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> Ahmet Yıldırım
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