Torsion dynamics

Luke M. Rice luke at laplace.csb.yale.edu
Mon Nov 10 11:27:36 EST 1997


Hi.

	The maxlen parameter can only be set within the topology statement.  If
the input attached with the original message is correct, then there
should be an additional error message in the output file.  If moving the
'maxlen = 5000' statement (and in fact even something like 'maxlen =
300' should probably be fine) into the topology statement does not fix
the problem, feel free to mail again.

Luke Rice




0 wrote:
> 
> Hi all,
> 
> I'm trying to use XPLOR for a simulation of Phi/Psi-dynamics via the
> 'dynamics torsion' feature. I get problems with the setup as XPLOR
> terminates with a MAXLEN error which neither Michael Nilges nor I do
> understand. I think that I might have gotten the torsion topology setup
> wrong. I would be very grateful if anybody of you sees the error I make...
> Here's the dynamics torsion statements; a protein with 89 residues has been
> read in (segid  's042') and I want keep only the Phi/Psi for the
> dynamics. My idea is to fix all torsions first, then free Phi/Psi
> explicitly.
> 
> ============================== tors.xplor
> ! read in two segments (segid 'a000','s042') before
> ! fix all torsions first, then iterate over all Psi angles and free them explicitly
> dynamics torsion
>         maxlen = 5000
>         topology
>                 fix group ( all )  ! first keep all torsions rigid
>                 evaluate ( $ii = 1. )
>                 while ( $ii < 89 ) loop resnr
>                         evaluate ( $ii1 = $ii + 1)
>                         free torsion    (segid "s042" and resid $ii and name N)
>                                         (segid "s042" and resid $ii and name CA)
>                                         (segid "s042" and resid $ii and name C)
>                                         (segid "s042" and resid $ii1 and name N)  ! Psi
>                         ! and now the same for Phi.... not shown
>                         evaluate ( $ii = $ii + 1 )
>                 end loop resnr
>         end
> end
> dynamics torsion
>         maxlen = 5000
>         reassign = true
>         tbath = 300
>         trajectory=./tors.dcd
>         nstep=1000
>         nprint=100
>         nsavc=100
>         nsavv=10
>         ntrfrq=10
> end
> 
> ============================== tors.xplor
> 
> XPLOR terminates with the following:
> 
> ============================== XPLOR's last words
> 
>  -------------------------- Torsion Topology ----------------------------------
>    WARNING: A chain is too long.
>             Please increase MAXLEN and re-run.
> 
>  %TORSION:TOPOLOGY-ERR: Fatal Topology Error
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  BOMLEV=    0 reached.  Program execution will be terminated.
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>  Subroutine DIE called . Terminating
> 
> ============================== XPLOR's last words
> 
> Hmmm. As I set MAXLEN to 5000 already I can't really imagine the chain to
> be too long (89 residues should give 178 free torsions if bot Phi/Psi are
> considered). Can it be that my way of specifying free torsions (first fix
> them all, then explicitly free those you want to simulate) doesn't work as
> the same torsion might be kept in the fixed as well as in the free list?
> What would be the 'right' way of running Phi/Psi dynamics with XPLOR?
> 
> Greetings,
> 
>         Lutz Ehrlich
> 
> ----------
> Lutz Ehrlich
> EMBL
> Meyerhofstr. 1
> D-69112 Heidelberg
> 
> email: lutz.ehrlich at embl-heidelberg.de
> web  : http://www.embl-heidelberg.de/~ehrlich
> phone: +49-6221-387-140
> fax  : +49-6221-387-517



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