[gmx-users] define terminal residue ?

[Justin Lemkul]

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

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

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