I am trying to build a mask to use in a QM/MM simulation. The purpose of the mask is to identify the QM region.
My system consists of a solvated, charge neutralized DNA molecule.
I have been working on the mask I want to use as the qmmask variable. I have been using the ambmask function to define the mask so the atoms I include in the QM region are the ones in which I am interested.
If I do this:
ambmask -find -p prmtop -c inpcrd -find ':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+)' > test.pdb
I generate a pdb file with this header:
natom = 18490
nres = 4515
original : ==:5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:15.0 & :Na+);==
tokenized: ==[:5-7,16-18]|([:5-7,16-18]<[:5.0]&[:WAT])|([:5-7,16-18]<[:15.0]&[:Na+]);==
postfix : ==[:5-7,16-18][:5-7,16-18][:5.0]<[:WAT]&|[:5-7,16-18][:15.0]<[:Na+]&|;==
379 atoms selected
REMARK :5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:15.0 & :Na+);
Note: 379 atoms are selected.
However, if I use this as my sander input file:
cgataaatagc : Frame 1000 QMMM test
&cntrl
imin=0, ntb=1
cut=8.0, ntc=2, ntf=2,
tempi = 310.15, temp0 = 310.15,
ntt = 3, gamma_ln = 1.0,
nstlim=0, dt=0.002,
ntpr=1, ntwx=1,ifqnt=1
/
&qmmm
qmmask=':5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+)',
qmcharge=0,
qm_theory='EXTERN',
qmshake=0,
qm_ewald=0,
writepdb = 1
/
&orc
basis = 'sto-3g',
method = 'hf',
num_threads = 30
/
With the command line:
sander -O -i AAA_salt_qmmm_orc.in -o AAA_salt_qmmm_orc.out -p AAA_salt.prmtop -c inpcrd -r AAA_salt_qmmm_orc.rst
I get the attached output file which contains, at its end, this:
LOADING THE QUANTUM ATOMS AS GROUPS
Mask :5-7,16-18 | (:5-7,16-18 <:5.0 & :WAT) | (:5-7,16-18 <:9.0 & :Na+); matches 17964 atoms
PARAMETER RANGE CHECKING:
parameter QMMM: (number of quantum atoms) has value 17964
This is outside the legal range
Lower limit: 1 Upper limit: 10000
Note: 17964 atoms are selected.
Would someone please help me figure out why the mask works with ambmask but not qmmask?
Thanks.
Jim
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Received on Tue Feb 20 2018 - 16:30:03 PST
