Re: [AMBER] NUCGEN and FORCE Field disfunction

From: Jason Swails <jason.swails.gmail.com>
Date: Thu, 19 Apr 2012 07:55:48 -0400

Hello,

Don't use nucgen -- it's very old and does not work with the newest versions of the Amber force field libraries since the pdb standard has changed (and nucgen was not updated).

Tutorial b1 (ambermd.org/tutorials/basic/tutorial1/section2.htm) doesn't use nucgen anymore--it uses nab.

However, xleap shouldn't segfault with a misnamed pdb, so I'm not sure what is happening here...

Another suggestion is to upgrade to AmberTools 12 which is available on the Amber website.

HTH,
Jason 

--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
On Apr 19, 2012, at 6:00 AM, VladanStefanovic.kg.ac.rs wrote:
> Hi,
> 
> 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:
> www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section2.htm;
> 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.
> 
> Thanks,
> Vlada
> 
> 
> 
> 
> 
> 
> 
> 
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Received on Thu Apr 19 2012 - 05:00:04 PDT
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