Inconsistent atom count

From: Laura Joana (
Date: Tue Jul 05 2016 - 12:04:44 CDT

Dear users,

I'm having a ridiculous problem and I have no idea why.
I did a 200 ns simulation using a pdb file and stored the last state to
restart the simulation. I could restart the simulation without a problem,
but if I try to read the coordinate file for the last state using VMD and
passing the same psf file it gives me "Inconsistent atom count". Strange,
right? I thought the problem should be with VMD as NAMD started the
simulation using the same coordinate and psf files without a problem.
Then, using the dcd and veldcd files from my first simulation I extract one
of the frames using VMD. Now I'm trying to start a new simulation from this
point and guess what NAMD is saying now: "Number of pdb and psf atoms are
not the same!". I also tried to read the coordinate file with VMD and it
gave me the same error as before.
Please, what am I missing here?
My system is just one molecule in vacuum and no periodic cell!


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