I am struggling with TI calculations using qmmm (DFTB method) for quite
some time now. I've had all sorts of different problems, but most of them I
could understand that what the cause was and, either work my way around or
fix it. Now I came across something I was not expecting to happen. I have
set my qmshake = 1 and a bond from one of the oxygens of an aspartic acid
side chain carboxyl group has broken. This residue is not part of my
softcore group of atoms, so, I believed that shake was actually being
applied to these atoms. And also, this atom was not supposed to fly around
(chemically speaking), there is not enough energy to break that bond. Some
help here would be great.
Here is the qm part of the input file:
&qmmm
qmmask=
':200,255,258&!.CA,C,HA,O,N,HN,H|:341,342|(:202,204&!.CA,C,HA,O,N,H)'
dftb_3rd_order = 'PA'
qmcharge=-1,
diag_routine=2,
qm_theory='DFTB',
qmshake=1,
qm_ewald=1, qm_pme=1
qmcut=9.0
writepdb=1
The softcore residue is 342 and the aspartic acid is residue 202.
Thank you
Fabrício Bracht
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Received on Tue Feb 19 2013 - 15:00:03 PST
