On 12/3/2013 10:13 AM, Hallel Freedman wrote:
> Dear AMBER,
> I just wanted to make sure my message went through to the list yesterday.
> Thanks,
> Holly
>
>
> On Mon, Dec 2, 2013 at 5:46 PM, Hallel Freedman <hfreedma.ualberta.ca>wrote:
>
>> Dear AMBER,
>>
>> I am setting up AMBER simulations of a proteins containing zinc fingers,
>> and I am trying to use the Zinc parameters from Yuan-Ping Pang, together
>> with the library and parameters downloaded from the website given on the
>> AMBER homepage:
>> When I try to save AMBER parm files I am getting messages like:
>>
>> 1-4: angle 43748 43749 duplicates bond ('triangular' bond) or angle
>> ('square' bond)
In calculating the 1-4 nonbonded exclusion lists it was found that you
have either three atoms bonded into a triangle, or four atoms bonded
into a square. Are the atoms printed?
>>
>> Is this anything to worry about?
>>
>> One other thing bothered me a little bit - when I try to solvate the
>> system I get messages like:
>> (using default radius 1.500000 for D4)
>> (using default radius 1.500000 for D3)
>> (using default radius 1.500000 for D2)
>> (using default radius 1.500000 for D1)
>> I suppose this is not important, but I wanted to confirm this with you.
This suggests you have atoms with no radius parameter defined, which
might bite you later in saving prmtop.
Bill
>>
>> Thanks in advance,
>> Holly
>>
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Received on Tue Dec 03 2013 - 10:30:05 PST
