Hi Dan,
Thanks for the reply. It's actually fine, I just didn't wait long enough!!
Regards,
Lui
On 08/04/2011 16:59, Daniel Roe wrote:
> Hi,
>
> Ptraj can potentially have problems with very large files. A bugfix
> has been released that deals with some of these issues.
>
> Have you applied all of the bugfixes? Also, what is the size of the
> trajectory file? Thanks!
>
> -Dan
>
> On Fri, Apr 8, 2011 at 11:48 AM, Lui<ltl.cs.nott.ac.uk> wrote:
>> Dear all,
>>
>> I'm trying to use PTRAJ to calculate the distance between the different
>> residues.
>> The input file is simply:/
>>
>> trajin data.trj 1 4535 1
>> distance d1-2 :1 :2 out dis1.5.list/
>>
>> My data file is in the form of AMBER trajectory (also called AMBER
>> coordinate in VMD), uncompressed.
>> When I run PTRAJ, i get the following error
>>
>> /checkCoordinates(): Could not predict number of frames for AMBER
>> trajectory file: data.trj
>> If this is not a compressed file then there is a problem/
>>
>> The last line of the ptraj.out file is
>>
>> /Processing AMBER trajectory file data.trj/
>>
>> The trajectory file can be opened with VMD and the visual output looks
>> perfectly normal.
>>
>> I have used the same script and method for another trajectory file, and
>> it worked without any problem.
>>
>> I'm using AmberTools 1.4.
>>
>> Any suggestions?
>>
>> Thank you.
>>
>> Regards,
>> Lui
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>>
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Received on Fri Apr 08 2011 - 10:00:03 PDT
