On Wed, Aug 20, 2014 at 10:20 AM, Urszula Uciechowska <
urszula.uciechowska.biotech.ug.edu.pl> wrote:
> Dear Jason,
> Please download the ambpdbERROR.zip file which contains prod.prmtop and
> prod.rst from:
>
> https://www.sendspace.com/file/54qe5b
>
> Using those files I tried to run ambpdb command. I have also tried to use
> prod.rst file for the next production run.
>
There are ***s in your inpcrd file. Look at line 28587:
115.5537065************ 12.6537715 115.0636064************ 12.6532888
115.3578012************ 13.5033254-891.8520828 493.4722293 62.3942084
This indicates that you have an overflow as some coordinates got too
large. If you are using Amber 14, the error message from sander or pmemd
should indicate what went wrong and how to fix it (i.e., use iwrap=1 in
your input file).
Both Dave Case and I suggested that you look for "*" characters in your
inpcrd file in previous emails, which is a common problem that has been
discussed many times on this list previously. To save us all time, please
be sure to read the answers you get on this list carefully and try all of
the suggestions in the future, or ask for clarification if the suggestions
are unclear.
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Aug 20 2014 - 08:00:02 PDT
