I think we would need to see your exact error message; I have no idea what
you mean by "charge error".
One possible problem is that iqmatoms is generally not the recommended
option for selecting a qm region, you may be getting overflow in the
selection and therefore the selection that is actually used is not
necessarily the one you specified (this should be obvious from the output
and the pdb file). I would recommend qmmask instead.
HTH,
Brian
On Wed, Jul 1, 2015 at 1:00 PM, Brittany Boykin <
bzb0031.tigermail.auburn.edu> wrote:
> 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
>
--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Jul 01 2015 - 12:00:02 PDT
