I can reproduce the error and will work on a fix shortly.
In the meantime, you can strip the restart file using ptraj or cpptraj
(cpptraj can actually generate stripped topology files as well).
HTH,
Jason
On Thu, Feb 7, 2013 at 10:52 AM, Jio M <jiomm.yahoo.com> wrote:
> Dear All,
>
> I am trying to strip ions, using parmed.py, from prmtop (having ions and
> water) and restart and create new out files as follows:
>
> parmed.py a.prmtop <parm.in> parm.out
>
>
> where parm.in is:
> loadRestrt prod.rst
> strip .Cl-
> parmout del.prmtop del.inpcrd
>
> But I get some error like this: "IndexError: list index out of range"
>
> I just have 32 ions and also if I just remove waters (strip .WAT) it works
> fine. I tried in other manner also; first remove all waters then using
> water stripped prmtop I tried to remove ions even then I get same error.
>
> please suggest if something I am missing.
>
> regards,
> Jiom
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Feb 07 2013 - 08:30:03 PST
