From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Sat Jun 18 2016 - 09:20:09 CDT

I'm reading it from the directory the calculation is running in.

dcd file 2 is much larger than dec file 3.

Richard
________________________________________
From: Gianluca Interlandi [gianluca_at_u.washington.edu]
Sent: Friday, June 17, 2016 2:29 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.

Maybe the file was not transferred correctly to your desktop PC. Try
copying it again from where the simulation was run.

What is the filezise of membrane_MORS_autopsf_2.dcd and
membrane_MORS_autopsf_3.dcd?

Gianluca

On Fri, 17 Jun 2016, Richard Wood wrote:

> 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.
> -----------------------------------------------------

-----------------------------------------------------
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.
-----------------------------------------------------