[AMBER] NUCGEN and FORCE Field disfunction

From: <VladanStefanovic.kg.ac.rs>
Date: Thu, 19 Apr 2012 12:00:16 +0200


I'm using AMBER for the first time; I have installed AMBER11 with
AmberTools1.4 on 32bit ubuntu linux successfully.

Now I have problems with using program nucgen and force field files.
I learn how to use amber from ambermd.org/tutorials-TUTORIAL B1, and when
I type: $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB

it returns:
           -I: Adding /usr/local/amber11/dat/leap/prep to search path.
           -I: Adding /usr/local/amber11/dat/leap/lib to search path.
           -I: Adding /usr/local/amber11/dat/leap/parm to search path.
           -I: Adding /usr/local/amber11/dat/leap/cmd to search path.
           -s: Ignoring startup file: leaprc
           -f: Source leaprc.ff99SB.
            Segmentation fault

after that nothing happens.

Also I read tutorials from:
where I have problem running nucgen to create input coordinates pdb file.

$AMBERHOME/exe/nucgen -O -i nuc.in -o nuc.out -d
$AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb

doesn't work, amber doesn't recognize nucgen neither like command neither
like file.

If somebody has solutions then please explain to me.


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Received on Thu Apr 19 2012 - 03:30:03 PDT
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