[gmx-users] In the chosen force field there is no residue type for 'THR' as a standalone (starting & ending) residue
jalemkul at vt.edu
Fri Oct 27 16:34:07 CEST 2017
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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