Custom Search
-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Aug 4, 2011, at 2:00 PM, Molybdos Kirkimpolakis <supercomputer.simulation.gmail.com> wrote: > Dear All, > > Can anyone tell me if these 2 flags can be deleted without making any > change in the simulation? Do they convey important information for the > simulation? (SCEE_SCALE_FACTOR and SCNB_SCALE_FACTOR) > > Thanks so much for your help. > > 2011/8/4 Molybdos Kirkimpolakis <supercomputer.simulation.gmail.com> > >> Hi Jason, >> >> Thanks so much for your reply. These two new flags are the reason why NAMD >> does not recognize the Top file generated by AmberTools 1.5 . I am copying >> the error message below >> >> I don't know If there was a difference. I concluded that there may be some >> slightly difference because NAMD fails to read the Top file generated by >> AmberTool 1.5; but has no problem reading a Top file generated by AmberTool >> 1.2 >> >> I guess these two new flags were confusing NAMD. I deleted them and now >> NAMD has no problem reading the top file. >> >> However my concern is that can these 2 flags be deleted without making any >> change in the simulation? Do they convey important information for the >> simulation? >> >> Thanks so much for your help. >> >> >> ######################################################## >> .................................. >> Info: RIGID WATER USING SETTLE ALGORITHM >> Info: RANDOM NUMBER SEED 1312401187 >> Info: USE HYDROGEN BONDS? NO >> Info: Using AMBER format force field! >> Info: AMBER PARM FILE system.top >> Info: AMBER COORDINATE FILE system.coor >> Info: Exclusions will be read from PARM file! >> Info: SCNB (VDW SCALING) 2 >> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS >> Reading parm file (system.top) ... >> PARM file in AMBER 7 format >> FATAL ERROR: Failed to read AMBER parm file! >> ------------- Processor 0 Exiting: Called CmiAbort ------------ >> Reason: FATAL ERROR: Failed to read AMBER parm file! >> >> ############################################################ >> >> >> >> >> 2011/8/3 Jason Swails <jason.swails.gmail.com> >> >>> Error messages would help here. The format of the amber topology file has >>> not changed between AmberTools 1.2 and 1.5. However, a couple flags >>> (specifically SCEE_SCALE_FACTOR and SCNB_SCALE_FACTOR) have been added >>> since >>> then. >>> >>> What differences exist between the 2 topology files? >>> >>> We need some more information to offer any more help (though other >>> Amber/NAMD experts can probably help more here). >>> >>> HTH, >>> Jason >>> >>> 2011/8/3 Molybdos Kirkimpolakis <supercomputer.simulation.gmail.com> >>> >>>> Dear All, >>>> >>>> I have a problem using AmberTools 1.5 to generate the top and coor >>> files, >>>> and do simulations using NAMD. The problem is that NAMD 2.7 fails to >>> read >>>> the top file. However, when I used the top file generated by an old >>> version >>>> of amberTools 1.2, I have no such problem. NAMD can read the top file >>>> without problems. >>>> >>>> It looks that AmberTools 1.5 is writing top files in slightly different >>>> way, >>>> than previous versions so that NAMD cannot properly read the top file. >>>> >>>> Can anyone tell me if the formats for top and coor files are the same >>> in >>>> all versions? or this is a bug? Are there any document that explain >>> this >>>> variation in formats? >>>> >>>> Thanks so much for your help >>>> >>>> >>>> -- >>>> cheers >>>> >>>> Molybdos Kirkimpolakis >>>> >>>> Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr> >>>> >>>> ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ >>>> _______________________________________________ >>>> AMBER mailing list >>>> AMBER.ambermd.org >>>> http://lists.ambermd.org/mailman/listinfo/amber >>>> >>> >>> >>> >>> -- >>> Jason M. Swails >>> Quantum Theory Project, >>> University of Florida >>> Ph.D. Candidate >>> 352-392-4032 >>> _______________________________________________ >>> AMBER mailing list >>> AMBER.ambermd.org >>> http://lists.ambermd.org/mailman/listinfo/amber >>> >> >> >> >> -- >> cheers >> >> Molybdos Kirkimpolakis >> >> Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr> >> >> ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ >> >> >> > > > -- > cheers > > Molybdos Kirkimpolakis > > Πανεπιστήμιο Πατρών <http://www.biology.upatras.gr> > > ΤΜΗΜΑ ΒΙΟΛΟΓΙΑΣ > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Aug 05 2011 - 06:00:03 PDT