Re: [ccp4bb] [cnsbb] RE: [ccp4bb] CNS problem: anneal.inp segmentation fault

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: website back up
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2007-05-22

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Subject: Re: refmac runs, but no output files
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-23

Subject: Re: [cnsbb] RE: CNS problem: anneal.inp segmentation fault
From: William Scott wgscott {- at -} CHEMISTRY {- dot -} UCSC {- dot -} EDU
Date: 2007-05-23

Try using phenix, which is the successor to CNS.

phenix.refine foo.mtz bar.pdb

and Bob's your uncle.

http://www.phenix-online.org/

jean wrote:
> Thank you all for your suggestions. Unfortunately I am still stuck with
> the
> segmentation fault problem.
>
>
>
> The swap partition is mounted fine.
>
> Setting max_chains to a lower number does nothing.
>
> There's nothing wrong with my selection criteria (0 atoms were selected as
> rigid groups, 36 for annealing)
>
>
>
> I tried systematically deleting parts of the pdb input file, then
> rerunning
> generate.inp and then anneal.inp. That worked fine for my ligand alone
> (as
> I understand it, given the right toppar inputs, CNS should be able to run
> torsion dynamics on my ligand - am I right?), but the protein component
> caused failure again. I can't spot a problem by looking so I'm at a bit
> of
> a loss.
>
>
>
> Any more ideas?
>
>
>
> Sincerely
>
> Jean
>
>
>
> _____
>
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of jean
> Sent: 11 May 2007 12:45
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] CNS problem: anneal.inp segmentation fault
>
>
>
> Hi all
>
>
>
> Apologies for the non-ccp4 question - hopefully some of you who use CNS
> can
> help me - I have a problem with anneal.inp in CNS:
>
>
>
> When I run the anneal script for my structure containing novel ligand, the
> program fails before the start of the torsion dynamics with no error
> message
> - except SEGMENTATION FAULT at the bash commandline.
>
>
>
> With "quiet" output, the last lines in the output file are:
>
>
>
> ASSFIL: file /usr/local/CNS/cns_solve_1.1/libraries/toppar/torsionmdmods
> opened.
>
> MESSage=NORM
>
> EVALUATE: symbol $MESSAGE_OLD_TMOD set to "NORM" (string)
>
> ECHO=FALSe {OFF}
>
> EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical)
>
> NEXTCD: condition evaluated as false
>
> Program version= 1.1 File version= 1.1
>
> SELRPN: 0 atoms have been selected out of 4883
>
>
>
> so the torsionmods routine (and everything before it) ran fine but the
> torsion dynamics never started.
>
>
>
> My pdb, mtf, top and par files all work fine for minimization so I don't
> think there's anything wrong with them.
>
>
>
> I have been using CNSv1.1 on this Linux machine for some time so it's not
> a
> compile problem.
>
>
>
> I can run the same routine on the same PC, from the same script, with the
> same protein but with a different ligand and there's no fault.
>
>
>
> Can anyone suggest a solution? I've tried just about everything short of
> running the whole script manually from the command line!
>
>
>
> Sincerely
>
> Jean Watermeyer
>
>
>
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: website back up
From: Bart Hazes bart {- dot -} hazes {- at -} UALBERTA {- dot -} CA
Date: 2007-05-22

Next message:
Subject: Re: refmac runs, but no output files
From: Ronan Keegan r {- dot -} m {- dot -} keegan {- at -} DL {- dot -} AC {- dot -} UK
Date: 2007-05-23