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
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Received on Thu Aug 04 2011 - 11:30:02 PDT
