VMD-L Mailing List

From: Richard Wood (Richard.Wood_at_purduecal.edu)
Date: Mon Jun 20 2016 - 07:47:38 CDT

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