Hi Jacopo,
Look at the file at:
$AMBERHOME/dat/slko/DISPERSION.INP_ONCHSP
There's a line for each atom. In the case of hydrogen,
H 0.386 0.386 0.000 0.000 3.5 3.5 3.5 3.5 0.8
The first 4 columns are parameters for when the atom is coordinated to 1,2,3 or 4 atoms. Which one is to be used is decided by counting the number of neighbours within a certain radius.
It appears that, at some point, it is counting 3 neighbours for the hydrogen within the radius, then it gets the zero.
One hack is to modify the third parameter, maybe to 0.386 as the 2 first ones. Of course, that is hoping it won't happen often…
HTH,
Gustavo Seabra
On Fri Nov 16 2012 08:07:31 Jacopo Sgrignani said:
> Hi Gustavo
> atom 26 is the hydrogen that is transferred in the reaction than it
> change its atom type during the reaction.
> When the simulation starts it is in the OH group of a serine but after
> the reaction it is bound to one N atom of an histidine residue.
>
> Jacopo
>
> 2012/11/16, Gustavo Seabra <gustavo.seabra.gmail.com>:
>> Hi Jacopo,
>>
>> What is atom 26? Not all atoms are parametrized with dispersion parameters.
>>
>> Gustavo Seabra
>>
>>
>>
>> On Fri Nov 16 2012 06:51:09 Jacopo Sgrignani said:
>>>
>>> Dear All
>>> I'm running a QM/MM (QM=DFTB, dispersion parameters and 3rd order "PA"
>>> corrections) simulation to study an enzymatic reaction, (in particular
>>> a proton transfer reaction).
>>> However during the calculation I get this error :" WARNING: a
>>> parameter is 0.0 for atom 26"
>>> could anybody explain me the meaning of the warning?
>>> Are there some ways to avoid it?
>>> Thanks a lot
>>>
>>> Jacopo
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 16 2012 - 03:30:03 PST
