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

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

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From: James Irving irving {- dot -} james {- at -} GMAIL {- dot -} COM
Date: 2007-05-22

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Subject: Re: CNS problem: anneal.inp segmentation fault
From: jean jean {- at -} SCIENCE {- dot -} UCT {- dot -} AC {- dot -} ZA
Date: 2007-05-22

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: Re: twwining operator
From: James Irving irving {- dot -} james {- at -} GMAIL {- dot -} COM
Date: 2007-05-22

Next message:
Subject: Re: calc. of rots to align recip. space axes w/ beam
From: Boaz Shaanan bshaanan {- at -} BGU {- dot -} AC {- dot -} IL
Date: 2007-05-22