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-request at nmr.cit.nih.gov wrote: > Send Xplor-nih mailing list submissions to > xplor-nih at nmr.cit.nih.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > or, via email, send a message with subject or body 'help' to > xplor-nih-request at nmr.cit.nih.gov > > You can reach the person managing the list at > xplor-nih-owner at nmr.cit.nih.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Xplor-nih digest..." > > > Today's Topics: > > 1. Re: Problems with eginput DNA structure calculations > (Charles at Schwieters.org) > 2. Re: Problems with eginput DNA structure calculations > (Charles at Schwieters.org) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 12 Feb 2010 16:15:37 -0500 > From: Charles at Schwieters.org > Subject: Re: [Xplor-nih] Problems with eginput DNA structure > calculations > To: "DeRose, Eugene (NIH/NIEHS) [C]"<derose at niehs.nih.gov> > Cc: xplor-nih at nmr.cit.nih.gov, "Charles at Schwieters.org" > <Charles at Schwieters.org> > Message-ID:<E1Ng2rR-0001BI-DO at tan.cit.nih.gov> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+<http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkt1xPkACgkQPK2zrJwS/larCgCZAYAA0tQZAA6sXI7yayuZS2pt > xhEAn08J5OYa3k3Ss7DbBfa7vqrj40SI > =8d4C > -----END PGP SIGNATURE----- > > > ------------------------------ > > Message: 2 > Date: Fri, 12 Feb 2010 16:32:05 -0500 > From: Charles at Schwieters.org > Subject: Re: [Xplor-nih] Problems with eginput DNA structure > calculations > To: "DeRose, Eugene (NIH/NIEHS) [C]"<derose at niehs.nih.gov> > Cc: "xplor-nih at nmr.cit.nih.gov"<xplor-nih at nmr.cit.nih.gov> > Message-ID:<E1Ng37N-0001NR-Ra at tan.cit.nih.gov> > > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > 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 > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.10 (GNU/Linux) > Comment: Processed by Mailcrypt 3.5.8+<http://mailcrypt.sourceforge.net/> > > iEYEARECAAYFAkt1yNAACgkQPK2zrJwS/laQsQCfZu6NBHVoLXIPfZr5VEB8hrHY > UuQAn0G+J5GwGuHp3UkyDmjSo99qg8E2 > =v6nX > -----END PGP SIGNATURE----- > > > ------------------------------ > > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih > > > End of Xplor-nih Digest, Vol 84, Issue 6 > **************************************** > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20100214/b17127cd/attachment.html
