Hi Thomas,
thanks so much! I feel dumb now lol.
Much appreciated Daniel and Thomas!
-Dave
On 7/19/11, Thomas Cheatham <tec3.utah.edu> wrote:
> I think it is a typo: mdrcrd ??? (ie check spelling on that 10 trajectory
> in ptraj input)
>
> On Jul 19, 2011, at 11:29 AM, "David Condon" <dec986.gmail.com> wrote:
>
>> Hi Daniel,
>>
>> thanks for your prompt reply!
>>
>>> Have you tried running ptraj on just this file? Can you open it in a
>>> text editor like vi? Is there any reason to suspect that it is
>>> corrupted (e.g. the file size is shorter than expected or something)?
>>
>> I opened it and saw nothing different from the trajectories before and
>> after. The file is 110 MB.
>>
>>> You could try running ptraj with more verbose messages to see if you
>>> can get some more info on why the file cannot be opened:
>>>
>>> prnlev 5
>>> trajin md10.mdcrd
>>> go
>>
>> I tired this and the computer read in the file just fine! However, I
>> added the line "prlen 5" and "go" to the combine script but it still
>> can't open md10.mdcrd
>>
>> "Could not open file (md10.mdrcd) with mode (r)
>> trajin md10.mdrcd ignored; could not open file (md10.mdrcd)"
>>
>>> Also, what version of AmberTools are you running and what bugfixes
>>> have been applied?
>>
>> I can't tell which version of AmberTools is installed (if any). I am
>> running Amber9 with bugfix.all set up to 46.
>>
>> Thanks for your help,
>> -Dave
>>
>> On 7/19/11, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>> Hi,
>>>
>>> Have you tried running ptraj on just this file? Can you open it in a
>>> text editor like vi? Is there any reason to suspect that it is
>>> corrupted (e.g. the file size is shorter than expected or something)?
>>>
>>> You could try running ptraj with more verbose messages to see if you
>>> can get some more info on why the file cannot be opened:
>>>
>>> prnlev 5
>>> trajin md10.mdcrd
>>> go
>>>
>>> Also, what version of AmberTools are you running and what bugfixes
>>> have been applied?
>>>
>>> -Dan
>>>
>>> On Tue, Jul 19, 2011 at 9:11 AM, David Condon <dec986.gmail.com> wrote:
>>>> Hello Amber Experts,
>>>>
>>>> I am running the following script to combine trajectory files, with
>>>> $ptraj prmtop < combine:
>>>>
>>>> trajin md3.mdcrd
>>>> trajin md4.mdcrd
>>>> trajin ...
>>>> trajin md12.mdcrd
>>>> trajout mdall.mdcrd
>>>>
>>>> For reasons beyond me, there is something wrong with md10.mdcrd:
>>>>
>>>> PTRAJ: trajin md9.mdcrd
>>>> Checking coordinates: md9.mdcrd
>>>>
>>>> PTRAJ: trajin md10.mdrcd
>>>> Checking coordinates: md10.mdrcd
>>>> Could not open file (md10.mdrcd) with mode (r)
>>>> trajin md10.mdrcd ignored; could not open file (md10.mdrcd)
>>>>
>>>> PTRAJ: trajin md11.mdcrd
>>>> Checking coordinates: md11.mdcrd
>>>>
>>>> Similar error messages are in the AMBER archives, but I did specify
>>>> the prmtop file (http://archive.ambermd.org/200503/0312.html) and the
>>>> permissions on all of the files are identical. This is a 64 bit
>>>> machine and the file is ~110 MB
>>>> (http://structbio.vanderbilt.edu/archives/amber-archive/2005/3108.php).
>>>>
>>>> Can this be fixed or do I have to re-run the simulation?
>>>>
>>>> Thanks for your time!
>>>> -Dave
>>>>
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>>>>
>>>
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Received on Tue Jul 19 2011 - 11:30:03 PDT
