AMBER Archive (2006)

Subject: AMBER: Shake&Lone Pairs

From: Lorenzo Gontrani (
Date: Wed Oct 25 2006 - 05:58:59 CDT

Dear AMBER users, does anybody have experience about using SHAKE when extra
points are defined on several atoms (C=O lone pairs)?
After equilibrating the water molecules box around my lone-pair containing
solute, I always get SHAKE errors whenever I release the solute constraints
(or I remove water BELLY). I checked with ptraj/checkoverlap and all the
short contacts are due to LP-heavy atom interactions.
Thanks for any help



Lorenzo Gontrani

CASPUR - Consorzio per le Applicazioni di Supercalcolo Per UniversitÓ e Ricerca via dei Tizii, 6 - 00185 Roma Tel +39 06 44486812 Fax +39 06 4957083 GSM +39 338 7615798 Email l DOT gontrani AT caspur DOT it

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