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 |
>
>
>
> __________________________________________________
> Do You Yahoo!?
> Tired of spam? Yahoo! Mail has the best spam protection around
> http://www.rosswalker.co.uk/adsense_alternatives/
> --------------------------------------------------------------
> ---------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Tue Sep 20 2005 - 22:53:00 PDT
