incorrect bond

From: Nadia Salami (
Date: Wed Sep 18 2013 - 01:28:59 CDT

Dear users,

I'm trying to build a monolayer APTES on a silicon nanowire (as a
functional group) in x direction, firstly I built a block of silicon (for
example 3 unit cells) then I passivated yx and zx surfaces of the silicon
block by OH group, after that I replaced hydrogen by silicon for APTES
group, finally I bounded neighbor APTES through O, according to the
attached figure, after these I replicated the built block by transitional
vector in x direction.
I merged pdb and psf files by VEGA ZZ,
but there are incorrect bonds between O and Si of the connected APTES,
I don't know how to build a correct model for silicon nanowires modified by
Please let me know if you have any idea regarding making a correct PSF file
for the new merged structure.




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