Re: [AMBER] error when doing lifetime calculation

From: Daniel Roe <>
Date: Mon, 23 Mar 2015 08:32:08 -0600


On Mon, Mar 23, 2015 at 12:32 AM, Vijay Achari <> 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.


> I am running this calculation in Centos 6.3 with 96 GB memory.
> Regards
> Vijay
> _______________________________________________
> AMBER mailing list

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Mon Mar 23 2015 - 08:00:03 PDT
Custom Search