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

[Ahmet yıldırım]

4 letter residue names of termini in pdb file are in the columns 18-22. I
think they are correct columns?

2015-02-06 13:15 GMT+01:00 Mark Abraham <mark.j.abraham at gmail.com>:

> 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
>
>
> >
> > --
> > Ahmet Yıldırım
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-- 
Ahmet Yıldırım