html manual 2.8, ref 46 and some GBIS questions

From: Branko (
Date: Sun Mar 20 2011 - 09:05:27 CDT


In html version of nightly build 2.8 release, reference 46 citation
(that do not exist), should be as follows:
Journal citation should be as follows: Proteins: Structure, Function,
and Bioinformatics (2004), 55(2), 383-394


I need to simulate small flexible molecules in implicit EtOH, is below
given parameters are suitable for such simulation; also can similar
parameters be used for heating (molecules are minimized on semiempirical
level with implicit solvation, so probably heating can be performed
without prior minimization)

#GBIS parameters
solventDielectric 24.3
ionConcentration 0
intrinsicRadiusOffset 0.09
GBISDelta 1.0
GBISBeta 0.8
GBISGamma 4.85
alphaCutoff 14
#nonbonded parameters
switching on
switchdist 16
cutoff 18
pairlistdist 19

Thank you in advance


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