Re: [AMBER] completing C-term atoms after strip in ptraj

From: Nihal Korkmaz <>
Date: Fri, 12 Oct 2012 13:48:36 -0500

I will do MMGBSA afterwards (strip :61-93 did not work in so
I would like to add the OXT atom to have more physically reasonable
results. I could just create pdbs and run them through tleap and
complete the C-term but that will be a bit time consuming. Is there any
command that I can include in ptraj after stripping to tell Amber to add
that OXT atom like tleap does?

Nihal Korkmaz

On 10/12/2012 1:38 AM, Jason Swails wrote:
> On Fri, Oct 12, 2012 at 1:53 AM, Nihal Korkmaz <>wrote:
>> Dear all,
>> I stripped the C-terminal of my protein from the trajectory by saying
>> "strip :61-93" with ptraj. However, the C-terminal is left as -CO, I
>> want to add an OXT so that it would be compatible with truncated
>> topology that I get with tleap.
> You can create a new topology file in by using exactly the same
> command (strip :61-93). This topology file will be compatible with your
> stripped trajectory file.
> Note, though, that while sander/pmemd *should* let you run simulations
> using this topology file, your system will be nonphysical. This is really
> for visualization and analysis applications.
> HTH,
> Jason

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Received on Fri Oct 12 2012 - 12:00:04 PDT
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