Hi Jacopo,
Note that there are 2 (incompatible to my knowledge) methods of selecting
the qmregion, "iqmatoms" and "qmmask". The first is an atom index list of
the atoms to include (which sounds like what you want) and the second is an
ambmask expression (perhaps used most commonly for selecting residues).
Are you using the proper namelist variable?
An important thing to consider is that arbitrary atom selections will not
necessarily have integer MM/RESP charges if the charges are taken from
standard libraries. Since meaningful quantum calculations require that
this be true, the codes usually impose it (they might even make checks
against the value set for "qmcharge," default is zero). The remaining
non-integer MM charge is then, by default, re-allocated amongst the MM
region in a physically specious way (that's not to insult the approach, it
is the simplest procedure that can be assured to work stably and
automatically).
In general, if you do not plan to select entire MM residues for the QM
region, then I would recommend composing your own custom residue(s) so that
the charges are integer without any re-allocation.
Regards,
Brian
On Tue, May 8, 2012 at 5:20 PM, Ben Roberts <ben.roberts.geek.nz> wrote:
> Hi Jacopo,
>
> On 9/05/2012, at 8:45 AM, Jacopo Sgrignani wrote:
>
> > I'm trying to prepare an input for a qm/mm calculation, anyway I'm not
> > able to consider only the residue side chains and the phosphate group
> > of the DNA.
> > I tried to specify the atomic index of the phosphate but the
> > calculation and when the QM atom are assigned, but if I specify the
> > entire residues
> > the calculation runs.
> > Is it mandatory to specify entire residues or is it an error in the
> > syntax I'm using?
>
> In order to answer your question we'll need to see your input, starting
> with the
> mdin file.
>
> Ben
>
>
>
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--
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Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
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Department of Chemistry : Piscataway, NJ
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Received on Wed May 09 2012 - 11:30:03 PDT
