On Fri, Oct 12, 2012 at 1:53 AM, Nihal Korkmaz <enihalkorkmaz.gmail.com>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 parmed.py 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
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Oct 12 2012 - 00:00:03 PDT
