[Xplor-nih] Problems writing output structures

[R.M. van der Werf]

Hi,

When I run a structure refinement, I write outputfiles, either accepted 
(extension *acc.pdb) or rejected (extension *.pdb).
out of 197 structures 141 are accepted, and at structure 142, I get the 
following error message (marked in bold):

 EVALUATE>($filename="result/fold_"+encode($count)+"_acc.pdb")
 EVALUATE: symbol $FILENAME set to "result/fold_142_acc.pdb" (string)
 X-PLOR>   set print-file=$filename end
*%ASSFIL-ERR: no free unit available
 %ASSFIL-ERR: Error accessing file*
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 BOMLEV=    0 reached.  Program execution will be terminated.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 Subroutine DIE called . Terminating

What is wrong ? Memory problems ? Or is something in the script wrong ?
Any suggestions are welcome.

Thanks,
Ramon

On 13-Feb-10 18:00, xplor-nih-requ...@nmr.cit.nih.gov wrote:
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Today's Topics:

    1. Re: Problems with eginput DNA structure calculations
       (char...@schwieters.org)
    2. Re: Problems with eginput DNA structure calculations
       (char...@schwieters.org)


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Message: 1
Date: Fri, 12 Feb 2010 16:15:37 -0500
From: char...@schwieters.org
Subject: Re: [Xplor-nih] Problems with eginput DNA structure
        calculations
To: "DeRose, Eugene (NIH/NIEHS) [C]"<der...@niehs.nih.gov>
Cc: xplor-nih@nmr.cit.nih.gov,  "char...@schwieters.org"
        <char...@schwieters.org>
Message-ID:<e1ng2rr-0001bi...@tan.cit.nih.gov>

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Hello Eugene--

   
When I generate the structure file using the old generatedna.inp script in =
the tutorial directory, the energies are much better and the structure is n=
ot distorted, i.e.,
     
How does that psf compare with eginput/dna_refi/dna_new.psf?

thanks--
Charles
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Message: 2
Date: Fri, 12 Feb 2010 16:32:05 -0500
From: char...@schwieters.org
Subject: Re: [Xplor-nih] Problems with eginput DNA structure
        calculations
To: "DeRose, Eugene (NIH/NIEHS) [C]"<der...@niehs.nih.gov>
Cc: "xplor-nih@nmr.cit.nih.gov"<xplor-nih@nmr.cit.nih.gov>
Message-ID:<e1ng37n-0001nr...@tan.cit.nih.gov>

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Hello again Eugene--

   
I am trying to use the dna_refi.inp script to compute the structure of the
Dickerson dodecamer with some ribose sugar substitutions.  Unfortunately the
structures, especially the base geometries are significantly distorted.

     
I think the issue is indeed a topology file mismatch. In
refine_full.inp, please replace nucleic.top/par with
nucleic-1.0.top/par, and do this to refine_full.py: add these lines:

protocol.topology['nucleic'] = "nucleic-1.0.top"
protocol.parameters['nucleic'] = "nucleic-1.0.par"

before the protocol.initParams line. I previously made this change to
ensemble.py, but forgot to update the other files.

The starting structure is not consistent with the current
topology/parameters. Please let me know if this clears things up.

best regards--
Charles
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