Hi Brian
thanks for your reply.
iqmatoms is the option I was looking for.
Jacopo
2012/5/9 Brian Radak <radak004.umn.edu>:
> 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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>
>
>
> --
> ================================ Current Address =======================
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--
Jacopo Sgrignani PhD
CNR-IOM-Democritos National Simulation Center
c/o International School for Advanced Studies (SISSA/ISAS)
via Bonomea 265,
34136
Trieste
Italy
email: sgrigna.sissa.it
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Received on Wed May 09 2012 - 12:00:04 PDT
