AMBER Archive (2004)

Subject: AMBER: pbsa

From: Chenglong Li (chenlong_at_scripps.edu)
Date: Thu Apr 15 2004 - 12:26:51 CDT

Hi,

I'm experimenting pbsa with RADIOPT=1 in amber8 and found:

a) if small moleclue included either alone or with protein, PB bombed
with "pb_aaradi(): ZERO sigma found for non-hydrogen atom";
b) if protein alone, PB initialization passed, but bombed next with
"pb_reslist(): maxnbr too small".

so it looks that there is problem with small molecule prmtop generated
with antechamber/gaff/leap(?). And how about maxnbr? Increase cutres
because maxnbr = natom * (sqrt( cutres + 3.0d0 ))**3 / 3.0d0?

Thanks for help,
Chenlong

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