Dear Dan,
I found out that there are 27 empty white spaces between the columns of the
data file. So I reduced the only one empty white space.
Now this works for me.
I used command awk.
*awk '{$1=$1}1' file*
Thanks.
Vijay
On Mon, Mar 23, 2015 at 10:32 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Mon, Mar 23, 2015 at 12:32 AM, Vijay Achari <glycoamber.gmail.com>
> wrote:
> > Internal Error: Input line size > internal buffer size (16384)
> > Internal Error: Increase the size of BufferedLine::DEFAULT_BUFFERSIZE
> and recompile
>
> This error occurs when you have very long lines in your input data
> file (greater than 16k characters). If you have lines longer than this
> in your input data file, unfortunately the only workaround is to do as
> the error message suggests. I'll have to consider implementing a
> better fix in the future.
>
> > Can I get any help to resolve this error? If I run with smaller number of
> > frames (1000), I don't have problem.
>
> Since you don't get the error when you run with fewer frames, this
> makes me think that maybe the formatting in the file
> 'onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat' gets messed
> up at some point. Do you expect the lines to be longer than 16k
> characters? If not it's possible you're missing a newline (or several)
> somewhere in the file.
>
> -Dan
>
> >
> > I am running this calculation in Centos 6.3 with 96 GB memory.
> >
> > Regards
> > Vijay
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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>
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Received on Mon Mar 23 2015 - 09:30:02 PDT
