[ccp4bb] a question about CNS composite omit map

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Subject: "inclusion body"
From: shivesh kumar 2shivesh {- at -} GMAIL {- dot -} COM
Date: 2008-04-02

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From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-04-02

Subject: a question about CNS composite omit map
From: Melody Lin xtalin2007 {- at -} GMAIL {- dot -} COM
Date: 2008-04-02

Dear all,

Sorry this might be another naive, non-ccp4 question~
I was trying to make a composite omit map with CNS, but during torsion angle
dynamics, it always reports an "argument out of range" error like the
following:

------------------ step= 5 at 0.02000 ps
-----------------------------

E(kin)+E(total)=52920.147 E(kin)=234.290
temperature=200.000

Etotal =52685.857 grad(E)=17.535 E(BOND)=79.376
E(ANGL)=566.763

E(DIHE)=1157.267 E(IMPR)=122.802 E(VDW )=2908.858
E(PVDW)=67.125

E(HARM)=3.348
E(XREF)=47780.318

-------------------------------------------------------------------------------
TORMD: velocity rescaling (VSCAle) enabled
-------------------------- Torsion Angle Dynamics
-----------------------------
WARNING: Velocities taken from last torsion angle dynamics step.
-------------------------------------------------------------------------------
TORMD3: number of degrees of freedom= 1179
-------------------------- Initial Conditions
---------------------------------

E(kin)+E(total)=52765.760 E(kin)=175.717
temperature=150.000

Etotal =52590.043 grad(E)=17.162 E(BOND)=79.634
E(ANGL)=567.386

E(DIHE)=1158.107 E(IMPR)=122.945 E(VDW )=2897.021
E(PVDW)=66.611

E(HARM)=3.382
E(XREF)=47694.956

-------------------------------------------------------------------------------
NBONDS: found 80621 intra-atom interactions
NBONDS: found 3240 symmetry-atom interactions
%CHEVAL error encountered: argument out of range
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************

I have tried to increase the Torsion angle MD parameters, but while that
solved the problem for one other similar structure (a mutant), it doesn't
work for this structure I am talking about. I have two other similar
structures with similar resolution (around 2.1A), R/Rfree (0.22/0.24) values
and only differ by a couple of residues, and composite_omit_map was fine.

Could anyone explain to me what went wrong during these torsion angle
dynamics? How could I solve such problem?

Thank you very much!

Best,
Melody

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CCP4bb <-- 2008 <-- April 2008 <-- 02 April 2008

Previous message:
Subject: "inclusion body"
From: shivesh kumar 2shivesh {- at -} GMAIL {- dot -} COM
Date: 2008-04-02

Next message:
Subject: Re: "inclusion body"
From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-04-02