VMD-L Mailing List

From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Tue Jun 21 2016 - 06:12:17 CDT

No errors. One of the dcd files that I couldn't open a couple of days ago, I opened today.

________________________________________
From: Gianluca Interlandi [gianluca_at_u.washington.edu]
Sent: Monday, June 20, 2016 12:46 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.

Check the NAMD log! Any errors or warnings?

On Mon, 20 Jun 2016, Richard Wood wrote:

> Well, it's up and running.
>
> Richard
>
> ________________________________________
> From: Gianluca Interlandi [gianluca_at_u.washington.edu]
> Sent: Monday, June 20, 2016 12:23 AM
> To: Richard Wood
> Cc: John Stone; vmd-l_at_ks.uiuc.edu
> Subject: RE: vmd-l: Can't read DCD files generated using NAMD.
>
> Sounds like something's wrong with your computer? Try redoing the
> simulation.
>
> Gianluca
>
> On Sun, 19 Jun 2016, Richard Wood wrote:
>
>> The drive has 203 GB of free space.
>>
>> membrane_MORS_autopsf_2.dcd is 842, 249 KB
>> membrane_MORS_autopsf_3.dcd is 30,768 KB
>>
>> I've also noticed that I have three files that haven't been written to at all.
>>
>> Richard
>> ________________________________________
>> From: Gianluca Interlandi [gianluca_at_u.washington.edu]
>> Sent: Saturday, June 18, 2016 1:29 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.
>>
>> What is the exact file size of both files? It seems that something is
>> wrong with your system, like you might have run out of disk space, or for
>> some reason NAMD did not write to disk correctly. It's hard to say without
>> knowing the details.
>>
>> Gianluca
>>
>>> 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.
>>> -----------------------------------------------------
>>
>> -----------------------------------------------------
>> 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.
-----------------------------------------------------