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

Ahmet yıldırım ahmedo047 at gmail.com
Fri Feb 6 12:43:46 CET 2015

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.

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

Ahmet Yıldırım

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