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

From: Jason Swails <>
Date: Fri, 12 Oct 2012 08:38:08 +0200

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.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Fri Oct 12 2012 - 00:00:03 PDT
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