[gmx-users] pdb2gmx error due to terminal capping of peptide

[Mark Abraham]

Hi,

Leave the rtp the way it was and name the residue in the pdb file so that
it matches. Then you won't have to teach pdb2gmx that your newly invented
residue is protein

Mark

On Fri., 25 Jan. 2019, 05:51 Neena Susan Eappen, <
neena.susaneappen at mail.utoronto.ca> wrote:

> Hi GMX users,
>
>
>   1.  I drew the structure of my target peptide on Pymol, added amide
> capping group (NHH) at C terminus of peptide
>   2.  Typed in the command: gmx pdb2gmx –f A15K.pdb –o A15K.gro –ter –ignh
>   3.  Chose AMBER99sb-ildn force field which has parameters for NH2
> capping group
>   4.  Fatal error
>   5.  Changed naming of amide group in .rtp file of AMBER99sb-ildn from
> NH2 to NHH so that naming is similar to .pdb file.
>   6.  Still fatal error.
> The residues in the chain ALA16--NHH32 do not have a consistent type. The
> first residue has type 'Protein', while residue NHH32 is of type 'Other'.
> Either there is a mistake in your chain, or it includes nonstandard residue
> names that have not yet been added to the residuetypes.dat file in the
> GROMACS library directory.
>
> Any insight would be appreciated,
> Thank you,
> Neena
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>