I found and fixed the bug. The bugfix should be up shortly.
Thanks for the report!
Jason
On Thu, Feb 7, 2013 at 11:13 AM, Jason Swails <jason.swails.gmail.com>wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 07 2013 - 13:00:02 PST
