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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 03 2011 - 22:00:02 PDT
