VMD-L Mailing List

From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Fri Jun 17 2016 - 05:51:42 CDT

It says:

"read_dcdheader: premature end of file
ERROR) could not read file D:/NAMD/membrane_MORS_autopsf_3.dcd"

which is odd, because I can load the files membrane_MORS_autopsf_2.pdb and membrane_MORS_autopsf_2.dcd into VMD.
________________________________________
From: Gianluca Interlandi [gianluca_at_u.washington.edu]
Sent: Thursday, June 16, 2016 7:28 PM
To: Richard Wood
Cc: John Stone; vmd-l_at_ks.uiuc.edu
Subject: RE: vmd-l: Can't read DCD files generated using NAMD.

There should be a more detailed error message printed on the console,
e.g., if you started VMD from a terminal in Linux, it should print
someting like:

dcdplugin) read_dcdheader: corruption or unrecognized file structure
ERROR) Could not read file membrane_MORS_autopsf_3.dcd

Do you get that? If yes, then your DCD might be corrupted.

You can for example use `dumpdcd` to read the header.

Gianluca

On Fri, 17 Jun 2016, Richard Wood wrote:

> 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.
>
> Richard
>
>
> ________________________________________
> From: Gianluca Interlandi [gianluca_at_u.washington.edu]
> Sent: Thursday, June 16, 2016 6:36 PM
> To: Richard Wood
> Cc: John Stone; vmd-l_at_ks.uiuc.edu
> 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?
>
> Gianluca
>
> On Thu, 16 Jun 2016, Richard Wood wrote:
>
>> "Unable to load molecule."
>>
>>
>> ________________________________________
>> From: John Stone [johns_at_ks.uiuc.edu]
>> Sent: Thursday, June 16, 2016 3:02 PM
>> To: Richard Wood
>> Cc: vmd-l_at_ks.uiuc.edu
>> 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
>> vmd_at_ks.uiuc.edu
>>
>> 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
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>>
>
> -----------------------------------------------------
> Gianluca Interlandi, PhD gianluca_at_u.washington.edu
> +1 (206) 685 4435
> http://artemide.bioeng.washington.edu/
>
> Research Assistant Professor at the Department of Bioengineering
> at the University of Washington, Seattle WA U.S.A.
> -----------------------------------------------------

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

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