Hi everyone,
I am using the sander interface to run a QM calculation on one molecule
(Butanol- 15 atoms) in a box. I am including other molecules whose have
atoms that fall within a certain distance around the QM molecule as point
charges.
My input to sander (qm.in) looks as follows:
Testing tutorial on website for QMMM with Gaussian
&cntrl
imin=0,nstlim = 0, !do not run a minimization or MD run
ntb=2, !constant pressure periodic boundary conditions
ntf=2,ntc=2,
cut=10.0, !10 ang classic bond cutoff
ntp=1,
ifqnt=1 !switch on QM/MM
&end
&qmmm
qmmask='.16-30',
qmcharge=0,
qm_theory='EXTERN',
qmcut=10.0,
qm_ewald = 0 !Use a real-space cutoff for QM-QM and QM-MM long range
interactions.
&end
&gau
method = 'B3LYP',
basis = '6-31G* Freq',
&end
Atoms 16-30 here belong to the molecule that I want to calculate quantum
mechanically. Then I run the command:
sander -O -i qm2.in -o qm2.out -c ../../c2.inpcrd -p ../../../simbox.prmtop
I get several outputs including the file that sander used as an input to
Gaussian which I attached here (old.gau.job.inp). The beginning of the file
looks like this:
%chk=gau_job.chk
%NProcShared=1
%mem=256MB
#P B3LYP/6-31G* Freq SCF=(Conver=8) NoSymm Charge Prop=(Field,Read)
Gaussian run using SANDER external interface.
0 1
C 1.7629999999999992 -0.6445000000000007
0.6690000000000013
C 0.5479999999999994 -0.8485000000000007
-0.2869999999999987
C -0.4740000000000007 0.2914999999999993
-0.3389999999999986
C -1.8300000000000007 -0.0425000000000007
-0.8029999999999987
O -2.5260000000000002 1.1444999999999992
-1.0729999999999986
H -1.9130000000000005 1.7184999999999993
-1.5379999999999985
H 2.5259999999999994 -1.3325000000000007
0.3040000000000012
H 1.5289999999999992 -0.9005000000000007
1.7020000000000013
H 2.1819999999999995 0.3554999999999993
0.5600000000000012
H 0.0029999999999993 -1.7185000000000008
0.0770000000000013
H 0.8539999999999993 -1.0945000000000007
-1.3039999999999985
H -0.5540000000000007 0.6844999999999992
0.6740000000000012
H -0.0540000000000007 1.0024999999999995
-1.0509999999999988
H -1.6770000000000007 -0.6405000000000007
-1.7019999999999984
H -2.3290000000000006 -0.6755000000000007
-0.0689999999999987
11.6699999999999999 1.8194999999999990 2.9420000000000011
0.0914000055333610
10.7509999999999994 1.7334999999999996 1.8860000000000012
-0.5467999944666389
9.9049999999999994 1.5534999999999992 2.3030000000000013
0.4050000055333611
11.4599999999999991 2.8114999999999992 3.3430000000000013
0.0112000055333610
11.5770000000000000 1.0224999999999993 3.6800000000000010
0.0112000055333610
7.9059999999999988 -3.2045000000000008 1.3910000000000013
-0.1850999944666389
8.1440000000000001 -2.2615000000000007 2.5240000000000009
0.0026000055333610
7.8429999999999991 -0.7435000000000007 2.2410000000000014
-0.2023999944666389
...
>From what I saw online, this file starts off with a symbolic Z matrix which
should state the Cartesian coordinates of the atoms in the QM region (top
set of lines) and then the coordinates (and charge) of all the atoms
considered as point charges (second set of lines).
The issue is that there seems to be a manipulation of the coordinates before
this file is formed because these numbers do not match with the coordinates
in the inpcrd I give sander for neither the QM atoms or the point charges. I
also don't know how the charges are being calculated in this file since they
also don't match the prmtop file I included in the input.
Does anyone know how the input to Gaussian is generated by sander? I am
attaching all my files in this email in case they might help.
I would really appreciate any insight into this.
Thanks everyone,
--
Aseel Bala Ahmed
PhD Candidate, Chemical Engineering
Michigan State University
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- application/octet-stream attachment: qm2.in
- application/octet-stream attachment: qm2.out
- application/octet-stream attachment: c2.inpcrd
Received on Wed Jan 11 2017 - 14:00:02 PST
