Hello, I have a very similar problem like Martin. I tried to run water refinement with XPLOR-NIH 2.16.0 and used the example files from ftp://ftp.pasteur.fr/pub/BIS/linge/ to see whether it is running correctly but get the following error message after approx. 2 minutes in which it runs just fine. For my real case (155 residues plus organic non-bound ligand) I have tried water refinement with the recoord shell scripts and it was the same error message.
%ATMCHK-ERR: unknown coordinates for atom "WAT1-386 -TIP3-H1 " %ATMCHK-ERR: Unknown coordinates %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% BOMLEV= 0 reached. Program execution will be terminated. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Subroutine DIE called . Terminating Do you have any ideas what the problem might be? Help would be very much appreciated. Clemens -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hello Martin-- >/ > > />/ > > I have downloaded the waterrefine_XPLOR directory from Jens Linge's FTP />/ > site, />/ > > but I can't get the example to work; XPLOR does not read in the />/ > > dihedral angles and stops. />/ > />/ > if you could send me the URL from which you downloaded the example, and />/ > exact instructions on how to run it, I'll take a look at what's going />/ > on. />/ > />/ />/ The site is ftp://ftp.pasteur.fr/pub/BIS/linge/ />/ There is a directory "waterrefine_XPLOR" that contains all necessary files. / the DIHE restraint problem was a missing NASSign statement in read_data_test.xplor. Change the dihedral setup to restraints dihedral nass 2000 ! set echo off message off end @@dihed.tbl ! looking for the XPLOR bug: Are the dihedrals read in??? ? ! set echo on message on end end and things should work ok. The script doesn't appear to be particularly robust as it seems to blow up during dynamics unless I reduce the time stepsize to 0.001 ps. Use of the variable stepsize feature of the IVM would probably fix this, though. best regards-- Charles -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.6 (GNU/Linux) Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/> iD4DBQFGp5nKPK2zrJwS/lYRAthAAJYrswYagh63GgfVikj5gusZuxzhAJwP2yi9 DGmywQD8gkbG5nzB9xUxYA== =x0y -----END PGP SIGNATURE----- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20070814/92a3c193/attachment.html
