[gmx-users] In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residue

[Justin Lemkul]

On 10/27/17 5:22 AM, rose rahmani wrote:
> Hi GROMACS users
>
> I get the following error when i use pdb2gmx tool of GROMACS 5.4.1, with
> the AMBER03 ff.  command:
>   gmx pdb2gmx -f threonine.pdb -o threonine.gro -water spc
>
> error>>>In the chosen force field there is no residue type for 'THR' as a
> standalone (starting & ending) residue

The current form of the AMBER force field (at least, as implemented in 
GROMACS) does not support zwitterionic amino acids, because AMBER uses 
specific N- and C-terminal forms of amino acids. If parameters exist in 
the literature, you can add them to the .rtp file, otherwise use a 
different force field that actually supports such species.

> I attached my .pdb file here

The mailing list does not accept attachments.

-Justin

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Justin A. Lemkul, Ph.D.
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Virginia Tech Department of Biochemistry

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