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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Sep 09 2015 - 15:00:02 PDT
