Re: FATAL ERROR : Line too long in pdb file

From: Aron Broom (
Date: Fri Jun 15 2012 - 20:10:39 CDT

I am slightly confused by what you have written, but I think there are a
few points on which I can comment:

1) when you load binary coordinates and velocities, you need to supply a
PDB file as you say. But, that PDB file itself is NOT ignored, it is
simply that the coordinates from that file are not used. If the whole file
was ignored it wouldn't be needed. I'm not sure, but I believe it is
needed in order to assign the atoms and such, but then the actual values of
the x,y,z coordinates from the binary file are used.

2) You can easily check if your files are binary or not by opening them in
something like gedit, vim, or nano. If they are not binary, they should be
human readable, much like a PDB file. If they are binary they will not
be. In a lot of linux distros the thumbnail for a binary file will clearly
have 0's and 1's on it, rather than a preview of the text.

3) if you loaded the file as a bincoordinates, and the simulation actually
ran without giving all kinds of crazy velocity or constraint errors, than I
suspect it is fine. If the coordinates were totally messed up, you
wouldn't be able to just restart.

4) if you want to be really certain, load the questionable coordinates in
VMD. If it is ASCII, you will be able to load just the coordinates file on
it's own as PDB type, if it is binary, you'll need to load the PSF first
and the coordinates will then be loaded as NAMD or something like that.


On Fri, Jun 15, 2012 at 8:43 PM, <> wrote:

> Dear all,
> I am trying to restart my simulation from the restart coor and vel
> files.
> However I keep getting an error like "FATAL ERROR : Line too long in pdb
> file". I checked the archives and found that this may be because the coor
> file is binary and I may have to add a line bincoordinates and do the same
> for velocities. I did this and I was able to restart the simulation.
> However, I have a few doubts:
> 1) Why is a binary restart coor file being written when I have mentioned
> "binary
> output off" in my configuration file?
> 2)When a simulation run is finished, and the last coor and vel files are
> generated, then I am able to restart the simulation with coordinates and
> velocities (not bin). However I need to have bincoordinates to restart
> simulations from coor and vel files generated at various steps during the
> run.
> 3)I learnt from the manual that even when using bincoordinates, I need to
> have
> coordinates line in the configuration file however it will be ignored.
> Therefore, I tried to restart the simulation with some random name in the
> coordinates line but it complains of not finding the pdb file and works
> only
> when I mention the real file name (ionized.pdb)in the coordinates
> line.Does that
> mean that the original PDB and PSF files are being used to restart and not
> the
> restart.coor file?
> Any help will be appreciated.
> Amin.
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Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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