From: mdcooper (mdcooper_at_uvic.ca)
Date: Tue Oct 12 2004 - 18:52:43 CDT
Hi there,
I am to add one molecule of CO2 into my already minimized solvated system.
When I do so, no matter where it is placed, trying to start up a minimization
is impossible - I get:
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT
VDW BOUNDARY MISC KINETIC TOTAL TEMP
ENERGY: 0 2012.3514 1921.1975 1012.9252 21.8771 -64319.4483
6968.3134 0.0000 0.0000 0.0000 -52382.7838 0.0000
INITIAL STEP: 1e-006
GRADIENT TOLERANCE: -1.#IND
BRACKET: 0 0 -1.#IND -1.#IND -1.#IND
RESTARTING CONJUGATE GRADIENT ALGORITHM
I have built the psf and pdb file myself and I have used psfgen on the new pdb
file but both result in this problem.
ATOM 14109 H1 TIP3 9188 89.987 63.838 25.302 1.00 0.00 SOLV
ATOM 14110 H2 TIP3 9188 89.012 63.761 24.171 1.00 0.00 SOLV
ATOM 14111 C1 CO2 9199 12.769 58.845 29.385 1.00 0.00 SOLV
ATOM 14112 O1 CO2 9199 13.969 58.845 29.385 1.00 0.00 SOLV
ATOM 14113 O2 CO2 9199 11.569 58.845 29.385 1.00 0.00 SOLV
Has anyone encountered this before? As you can see the CO2 is well outside of
the protein sphere and yet the problem remains.
Thanks,
Matt
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