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 - 10:30:02 PDT
