Hi Francesco,
You might be better posting this question to the NAMD mailing list. However
the following error would appear to be telling:
> FATAL ERROR: Num of atoms in coordinate file is different from that in
> parm file!
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Num of atoms in coordinate file is different from
> that in parm file!
Did you try the CPU only version? Does it give the same error? - Have you
manually checked your prmtop and coordinate files to make sure the atom
counts match?
On another note why not just use GPU AMBER (PMEMD)? It is significantly
faster than the NAMD GPU version, especially on GTX580s where it screams!
and avoids all the complexities, and potential bugs or inaccuracies in
converting AMBER input files to NAMD.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Thu Oct 20 2011 - 00:30:03 PDT
