From: Richard Wood (
Date: Thu Jun 16 2016 - 19:17:04 CDT

Here's the text of my input file:

# This is a test namd configuration file

minimization on
structure membrane_MORS_autopsf.psf
paraTypeCharmm on
parameters par_all27_prot_lipid.prm
coordinates membrane_MORS_autopsf_3.pdb
numsteps 2000000
exclude scaled1-4
1-4scaling 0.4
outputname membrane_MORS_3_
binaryoutput no
cutoff 12.0
switching on
switchdist 7.0
DCDFILE membrane_MORS_autopsf_3.dcd
DCDfreq 1000

I read membrane_MORS_autopsf_3.pdb into VMD, then try to load membrane_MORS_autopsf_3.dcd where it asks the name of the file to load for this. When I click, "Load", I get the error message. This just started within the last two days.


From: Gianluca Interlandi []
Sent: Thursday, June 16, 2016 6:36 PM
To: Richard Wood
Cc: John Stone;
Subject: RE: vmd-l: Can't read DCD files generated using NAMD.

It sounds like the problem is with the PDB/PSF that you are trying to read
before the DCD. Could it be that you have renamed that?


On Thu, 16 Jun 2016, Richard Wood wrote:

> "Unable to load molecule."
> ________________________________________
> From: John Stone []
> Sent: Thursday, June 16, 2016 3:02 PM
> To: Richard Wood
> Cc:
> Subject: Re: vmd-l: Can't read DCD files generated using NAMD.
> Richard,
> Does VMD emit any particular error text when you try to load
> the file? It is possible that the file has been corrupted and
> the DCD header or one of the timestep markers has corruption
> that causes VMD to refuse to read it.
> Cheers,
> John Stone
> On Thu, Jun 16, 2016 at 04:12:53PM +0000, Richard Wood wrote:
>> I'm running some energy minimizations using NAMD and saving the
>> trajectories. Up until today, I was able to read these into VMD; as of
>> this morning, I am not able to and I don't know what the problem is. I've
>> not changed anything in the config file other than the names of the input
>> and output files.
>> Help!
>> Richard
> --
> 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

Gianluca Interlandi, PhD
                     +1 (206) 685 4435

Research Assistant Professor at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.