AMBER Archive (2009)

Subject: RE: [AMBER] [qm/mm] qmcharge for acidic a.a. in proteins

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 14 2009 - 14:45:06 CDT

Hi Yuann,

> Is the qmcharge for one GLU and one ASP residue involved in the qm
> region to be -2, while all the other residues in the mm region?
> I found that the part of output indicated that it was -1.637
> Although the calculation done without errors, I'm wondering if such
> adjusting is ok?

That is the million dollar question unfortunately. I'm not sure the answer
is strictly known and it really depends on what you ultimately plan to learn
from the simulation. What is happening here is that charge ultimately has to
be conserved but also the QM region has to have an integer charge. When you
define a QM region it zeros the charge of the MM atoms and 'replaces' them
with the QM region's integer charge. Thus if the atoms making up the
QM+MMlink region do not add up to an integer charge so you get some charge
left over that you have to do something with. At the moment you can have the
code take this difference and divide it up over the remaining atoms
(adjust_q=2) or place it on the nearest MM atoms to the link atoms.

Which one is better I think is a tough question. Ideally you should select
your QM region to minimize this difference in charge, i.e. in your case get
the QM+MM region resp charge sum you choose to be as close to -2 as
possible. Of course this also has the constraints that you should not break
double bonds and you really want as few link atoms as possible. Hence it is
a case of balancing the approximations. The optimum way to deal with QM/MM
covalent boundaries is still an area of active research.

So I am sorry if this doesn't help much but I think you just need to be
aware that this approximation was made and if you ultimately believe your
results might have been biased by it try repeating with a slightly different
QM region for example.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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