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
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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
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