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Re: [ccp4bb] CNS problem: anneal.inp segmentation fault |
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CCP4bb navigationCCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999Subject: Re: CNS problem: anneal.inp segmentation fault From: jean jean {- at -} SCIENCE {- dot -} UCT {- dot -} AC {- dot -} ZA Date: 2007-05-28 Hi all I seem to have got it to work, although the reason for the problem remains a mystery. There seems to have been an error in the protein component (by a process of elimination) of my pdb file that did not affect minimzation, but caused torsion angle dynamics to fail. In the end, I did a bit more building, output a new pdb file, used a new copy of generate.inp - and now it works. Thanks again to everyone who's been scratching their heads with me! Jean _____ From: cnsbb@yahoogroups.com [mailto:cnsbb@yahoogroups.com] On Behalf Of jean Sent: 22 May 2007 12:56 To: CCP4BB@JISCMAIL.AC.UK; cnsbb@yahoogroups.com Subject: [cnsbb] RE: [ccp4bb] CNS problem: anneal.inp segmentation fault 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! 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