Hello AMBER users,
I am using AMBER 14 to conduct QM/MM for a methyltransferase system. My system is methylated on either nitrogen, NH1 or NH2. I am having trouble with the qm-region in regards to charge error. The main problem in the qm-region is the substrate ARG332. I've tried numerous orders of the substrate in the qm-region (as shown below): Two different runs for constant volume held.
&qmmm
iqmatoms=1883,1884,1885,1886,1887,1888,1889,1890,1891,2038,2039,2040,2041,2042,2043,2044,2045,2046,4317,4318,4319,4320,4321,5319,5322,5323,5324,53
25,5326,5327,5328,5329,5330,5331,5333,5334,5343,5344,5345,5375,5376,5377,5378,5379,5380,5381,5382,5383,5384,5385,5386,5387,5388,5389,
qmcharge=0,
...skipping one line
qmshake=1,
qm_ewald=1, qm_pme=1,
diag_routine=0,
writepdb=1
/
EOF
&qmmm
iqmatoms=1883,1884,1885,1886,1887,1888,1889,1890,1891,2038,2039,2040,2041,2042,2043,2044,2045,2046,4317,4318,4319,4320,4321,5319,5322,5323,5324,53
25,5326,5327,5328,5329,5330,5331,5333,5334,5343,5344,5345,5372,5373,5374,5375,5376,5377,5378,5379,5380,5381,5382,5383,5384,5385,5386,5387,5388,5389,
qmcharge=0,
qm_theory='PM3-PDDG',
qmshake=1,
qm_ewald=1, qm_pme=1,
diag_routine=0,
writepdb=1
/
EOF
With these two different qm-regions with volume held constant, I am forced to change the qm-region when pressure and temperature is held constant (see below) due to charge error with original qm-region: Corresponds to one above.
&qmmm
iqmatoms=1883,1884,1885,1886,1887,1888,1889,1890,1891,2038,2039,2040,2041,2042,2043,2044,2045,2046,4317,4318,4319,4320,4321,5319,5322,5323,5324,53
25,5326,5327,5328,5329,5330,5331,5334,5343,5344,5345,5375,5377,5378,5379,5380,5381,5382,5383,5384,5385,5386,5387,5388,5389,
qmcharge=0,
qm_theory='PM3-PDDG',
qmshake=1,
qm_ewald=1, qm_pme=1,
diag_routine=0,
writepdb=1
My question is, why don't I have charge error when holding volume constant for equilibrating the system but have charge errors with the same qm-region stated in the constant volume when trying to run constant pressure and temperature? Also, in constant pressure and temperature, when I use a different qm-region than used in volume, the system does not fully converge.
Thanks in advance!
Brittany Boykin
Graduate Student
Auburn University
Department of Chemistry and Biochemistry
e: bzb0031.tigermail.auburn.edu
c: (404)545.1036
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Received on Wed Jul 01 2015 - 11:30:02 PDT
