[gmx-users] define terminal residue ?

Justin Lemkul jalemkul at vt.edu
Wed Jan 24 20:22:52 CET 2018

On 1/24/18 2:20 PM, MD wrote:
> Hi Gromacs,
> Can anyone give me a quick example to define the C-term residue? I have a
> complaint of OXT not defined in rtp and I think I probably should let
> gromacs know that is my c-term residue. I searched the tags and found this
> one "
> *-[no]ter* (no)
> Interactive termini selection, instead of charged (default)"
> But I couldn't find a real example to use this tag. My c-term SER358 is the
> one that causing this issue. Any help will be appreciated.

There's nothing special about them. If a normal amino acid is causing an 
issue, provide your command line and full screen output (please, in 
general, always do this with pdb2gmx problems - there's lots of output 
and experienced users can find subtle things quite quickly).



Justin A. Lemkul, Ph.D.
Assistant Professor
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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