Joshua Carr jkenne... at gmail.com
Wed Mar 25 19:21:21 UTC 2015

```Hello,

Does that mean the MM radii are the same for all MM_KIND's for the same
element? I'm concerned because based on JCTC 1, 1176 (2005), it seems that
the appropriate radius can vary somewhat substantially for the same element
in different bonding environments. That paper lists 1.2 A (for O) and 0.44
A (for H) as the appropriate radii for water (which add up to substantially
more than the OH bond length). Meanwhile, a table of covalent radii (e.g.
from the Cambridge Structural
Database, http://en.wikipedia.org/wiki/Covalent_radius) lists 0.66 A for O
and 0.31 A for H, almost a factor of 2 different for O. Moreover, the radii
ought to vary for different bonding environments. Although JCP 116, 6941
(2002) indicates that there is some tolerance for a range of values, it is
certainly possible to mess up the calculation by using bad values.

The best I can think to do now is use 1.2 A and 0.44 A for water, and use
values from the Cambridge Structural Database for all the protein atoms. Is
that reasonable? I feel this is probably not that big a deal, but I'm new
to QM/MM and am trying to ensure I don't make an error that will be
difficult to control for.

Thanks,

Josh

On Wednesday, March 25, 2015 at 10:48:44 AM UTC-5, Teo wrote:
>
> MM radii are just covalent radii (it’s very well explained in few papers).
> Find a table with covalent radii and you’ll have solved your problem
> (that’s what the mentioned script was doing)...
>
> Teo
>
> On 25 Mar 2015, at 15:29, Joshua Carr <jken... at gmail.com <javascript:>>
> wrote:
>
> I am having the same problem! I need to define radii for some new atom
> types, and I have no idea how to do so. Someone help, please!
>
> Josh Carr
>
> On Thursday, March 12, 2015 at 8:34:33 AM UTC-5, Kristof wrote:
>>
>> Hi all,
>> I am trying to set up a QMMM simulation, for which I will need the
>> covalent radii for the electrostatic coupling.
>> I found some old mails in this list that mentioned a "covalent_radii.pl"
>> script that is supposed to yield those. It is supposed to be in the files
>> section of this group.
>> However, I cannot find it (I can't find the files section for that
>>
>> Best,
>> Kristof
>>
>
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