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
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 03 2011 - 19:30:02 PDT
