Re: Running AMBER FF with NAMD 2.8-CUDA

From: Nicholas M Glykos (
Date: Wed Oct 19 2011 - 10:06:08 CDT

> True. That confirms my suspicion: should leap be run with special
> flags (for example for TIP3 water)? I just took the .prmtop/.inpcrd
> files mfrom the tutorial, and they surely work with AMBER.

Could it be your PBC box ? Your box appears to be 53.19 x 60.13 x 62.5 A^3
and you seem to load 211793 atoms.

          Dr Nicholas M. Glykos, Department of Molecular Biology
     and Genetics, Democritus University of Thrace, University Campus,
  Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620,
    Ext.77620, Tel (lab) +302551030615,

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