[AMBER] error when doing lifetime calculation

From: Vijay Achari <glycoamber.gmail.com>
Date: Mon, 23 Mar 2015 14:32:36 +0800

Dear Users,

I am trying to calculate HB lifetime. Total frames I am working with is
45000. When I run script below, I get some error. The script is below:

$top <<EOF readdata
onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat out

I get error as below:

*[vijay.glycogpu method-Daniel]$ ./4-process-lifeTime-hb-as-Daniel.sh
CPPTRAJ: Trajectory Analysis. V14.25 ___ ___ ___ ___ | \/ | \/ |
\/ | _|_/\_|_/\_|_/\_|_ Reading
'../../../../only-nc-Format-maltoLyo12per/maltoLyo12per.prmtop' as Amber
TopologyINPUT: Reading Input from STDIN [readdata
onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat] Reading
'onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat' as Standard Data
File with name
'onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.dat'Internal Error:
Input line size > internal buffer size (16384)Internal Error: Increase the
size of BufferedLine::DEFAULT_BUFFERSIZE and recompileError reading
datafile onlyData-hbLifeTime-maltoLyo12per-solulte-solute-O11.datError:
Could not read data file. 1 errors encountered reading input.TIME: Total
execution time: 0.0483 seconds.*

Can I get any help to resolve this error? If I run with smaller number of
frames (1000), I don't have problem.

I am running this calculation in Centos 6.3 with 96 GB memory.

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Received on Mon Mar 23 2015 - 00:00:03 PDT
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