There is also the problem that windows text editors appear to put unreadable characters into, particularly, ali files meaning that modeller doeasn't read them in the way you intended. Thus they look alright but are not. This has been reported to this list before. It would also suggest using Linux.
Nigel
Quoting Antoine Leimgruber antoine.leimgruber@etu.unil.ch:
> > > > Dear Jaimin, > > although I would be very carefull in saying that a top file and an ali > file are "alright", the problem might be somewhere else. > > I recall from you numerous emails that you are running under windows. I > did it once. From my experience, this is the time equation I get when > running on various platforms: > > 2.2Ghz linux athlon = 1 > powermac G5 = 1.3 > windows2000 700Ghz Athlon = 10++ > > I agree with you that this list is not a complete benchmark, put there > are two points: > > 1. I'm disappointed by the G5's performance, but this is not the > problem you are interested in. > 2. Windows was slow, i.e. more than 10 times slower than my mac > notebook G4 800GHz. Actually, it was so slow, that 10 times does not > mean anything at all. > > In conclusion, if you get stuck when generating the restraints (which > is a costly step anyway), it might actually work, but being so slow > you'd think it is stuck. At least if stuck does not mean "crashed". > Maybe RAM is the problem ? Is it swapping ? > I recall that you said it was working on a linux PC, but that you were > not very fond of using linux. Maybe you will loose less time learning > this very usefull OS rather than fighting against your windows PC ? ;-) > I strongly advise you to switch to linux. > > > BR > Antoine > > > > > > > > > Dear MODELLER users, > > > > Thank you for ur help so far. > > One problem still persists. MODELLER hangs at one point after some > > time: > > > > Dynamically allocated memory at amprmcns [B,kB,MB]: 17981749 > > 17560. > > 301 17.149 > > openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr > > openf5__224_> Open 11 OLD SEQUENTIAL galk.rsr > > > > The TOP and ALI files are alright. > > Please solve my problem. > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >
Dr. Nigel Lindsey Senior Lecturer in Biomedical Sciences Department of Biomedical Sciences University of Bradford Bradford W.Yorks
Tel +44 01274 233567
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