Re: vmd-l: Inconsistent atom count

From: John Stone (
Date: Tue Jul 05 2016 - 12:54:26 CDT

  It would be very helpful if you could tell us what version of VMD
you're using, what OS/platform you're running it on, and the specific
sequence of commands and/or file loading operations you performed and
the verbatim error messages that VMD emits in the text console.
VMD requires the same number of atoms in all files that are loaded into
the same molecule. The error from NAMD is basically the same. Is it possible
that you might have loaded the PDB file in an editor that did line wrapping
or some other damage to the file? If you load the PDB file by itself,
how many atoms does VMD say it contains? How about doing the same for
the PSF file?

On Tue, Jul 05, 2016 at 07:04:44PM +0200, Laura Joana wrote:
> 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!
> Bests,
> Laura

NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801           Phone: 217-244-3349      

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