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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>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Tue Jul 19 2011 - 11:00:05 PDT
