Hi David,
I had to solve this problem as well several times and for me at the end
[after experiments with pert true , bond command etc.] always worked only
increasing value of symbolic constant MAXBONDS
which is in file:
$AMBERHOME/AmberTools/src/leap/src/leap/atom.h
(and of course recompilation)
This symbolic constant has default value 8 , increasing it to 12 solved my
problems
e.g. in my Amber simulation study of titanocene.
Best wishes,
Marek
Dne Tue, 04 Apr 2017 21:53:23 +0200 Ben Roberts <ben.roberts.geek.nz>
napsal/-a:
> Hi David,
>
> I confess that it’s several years since I’ve used tleap in anger, but
> you could try the following:
>
> * use “pert=true” instead of “pert true” on the line in question
> * set a property “atoms pert=true” on a separate line, rather than
> associated with an individual particle
>
> Hope that helps,
> Ben
>
>> On 5/04/2017, at 2:23 AM, David Poole <thepoole.ucdavis.edu> wrote:
>>
>> Hello everyone,
>>
>> I've for some reason decided do something with Ferrocene in Amber,
>> because
>> it is fun? Anyway, tleap is kicking me a wonderful error when i try to
>> assign the ten bonds to the iron center:
>>
>>> bond x.1.Fe1 x.1.C32
>> Bond: maximum coordination exceeded on .R<MOL 1>.A<Fe1 54>
>> -- setting atoms pert=true overrides default limits
>>
>> And so I responded to tleap:
>>
>>> set x.1.Fe1 pert true
>>> bond x.1.Fe1 x.1.C32
>>
>> Which then I got the rude reply:
>>
>> Bond: maximum coordination exceeded on .R<MOL 1>.A<Fe1 54>
>> -- setting atoms pert=true overrides default limits
>>
>> On the off chance it could be reasoned with, I pleaded:
>>> set x.1.C32 pert true
>>> bond x.1.Fe1 x.1.C32
>>
>> Yet to no avail. Is there a hard-limit on the maximum coordination of an
>> atom type? or is it possible to change this limit somewhere/someway
>> else?
>>
>> Thank you kindly,
>>
>> -David
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Received on Tue Apr 04 2017 - 15:00:02 PDT
