Ross,
FYI we use > 2GB files on our 32-bit Pentiums in ptraj regularly.
Brent
On Sep 20, 2005, at 5:39 PM, Ross Walker wrote:
> Your file is bigger than 2 GB. While it is possible to compile
> programs to
> support large files on 32 bit machines I am not sure how 'clean'
> the ptraj
> code is with respect to using large file pointers.
>
> Therefore I suggest what you do is locate a 64 bit machine, copy
> the mdcrd
> file over to it and either process it there using ptraj or use
> ptraj on that
> machine to split the file into smaller chunks that you can then
> process on
> your 32 bit machine.
>
> This is an age old problem that should really no longer exist but
> the old 32
> bit chips seem to have hung on much longer than they should have.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery,
> may not
> be read every day, and should not be used for urgent or sensitive
> issues.
>
>
>> -----Original Message-----
>> From: owner-amber.scripps.edu
>> [mailto:owner-amber.scripps.edu] On Behalf Of Varsha Goyal
>> Sent: Tuesday, September 20, 2005 14:26
>> To: amber.scripps.edu
>> Subject: RE: AMBER: Could not open file (Melb.mdcrd) with mode (r)
>>
>> Dear Ross,
>> 1) I can't open mdcrd since size is too big (but i can
>> see all frames using VMD) and the permission looks
>> like this:
>> -rw-r--r-- 1 gupta users 25027560081 Aug 17 17:51
>> Melb.mdcrd
>> (may be size is really big)
>> 2) my trajin file looks like this
>> trajin Melb.mdcrd 19966 19966
>> trajout lowest_energy_struct.pdb pdb
>> 3) And i already took care of case.
>>
>>>
>>> A few questions...
>>>
>>> 1) Can you open Melb.mdcrd in the current working
>>> directory in something
>>> else? Like vi or emacs? Do you have permission to
>>> read the file?
>>>
>>> 2) Can you post your extract_frame.trajin file so I
>>> can check it?
>>>
>>> 3) Have you got the case correct? Most (all?) Unix
>>> machines are case
>>> sensitive while Windows machines are not. Thus on a
>>> Unix machine Melb.mdcrd
>>> and melb.mdcrd are different files while on a
>>> windows machine they will be
>>> treated as the same file. You should check this.
>>>
>>> All the best
>>> Ross
>>>
>>> /\
>>> \/
>>> |\oss Walker
>>>
>>> | Department of Molecular Biology TPC15 |
>>> | The Scripps Research Institute |
>>> | Tel: +1 858 784 8889 | EMail:-
>>> ross.rosswalker.co.uk |
>>> | http://www.rosswalker.co.uk | PGP Key available on
>>> request |
>>>
>>
>>
>>
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__________________________________________________________________
Brent P. Krueger phone: 616 395 7629
Assistant Professor fax: 616 395 7118
Hope College
Department of Chemistry
Holland, MI 49423
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Received on Wed Sep 21 2005 - 01:53:00 PDT
