Hi,
I am trying optimizing pyrophosphoric acid in implicit solvent with the method of SCC-DFTB. But after the optimization, the angle of P-O-P becomes 178.6 degree.
The initial structure of pyrophosphoric acid was got from PDBid 5erm, and the optimization was run by the qmmm module in sander with igb=2. To achieve a reasonable result, dftb_3rd_order='PR' and parameters downloaded from
https://dftb.org/parameters/download/3obophyd/3obophyd-1-2 were also tried but none of them gave a good result.
To get the benchmark, I optimized the structure in Gaussian with B3LYP/6-31g* level of theory and SMD method, and the result is 127.1 degree, which is 51.5 degree smaller then the result of sander. I also tried using DFTB+ with GBSA to study whether the strange result of sander was caused by the deficiency of SCC-DFTB. The result of DFTB+ was 140 degree, which is similar to the result of Gaussian.
Is this a bug of sander? How can I get a acceptable by sander?
Here is the input file
# test qmmm
&cntrl
ifqnt=1,
imin = 1,
maxcyc = 10000,
drms = 0.1,
ntpr=1,
ntwx=0,
ntb=0 ,
cut = 999.0,
igb=2,
/
&qmmm
qmmask=":1",
qmcharge = -4,
qmcut=999.0,
qm_theory="DFTB3",
spin=1,
writepdb=1,
qmshake=0,
/
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Received on Thu Apr 21 2022 - 20:30:02 PDT
