Brain slightly more engaged, it seems you are missing a residue
definition that likely already exists, you just would need to load a
.lib file for the residue, for example, before loadpdb. Probably an/the
(?) amber ion tutorial will be enough to help you fill in the blanks, if
you know your parameters and the relevant literature.
Bill
On 2/11/19 11:37 PM, Bill Ross wrote:
> Search on the web for calcium residue models (1-atom of course :-) for
> your C0 residue, which will assign an atom type.
>
> 'amber calcium ion' could get you started. You will want to
> compare/contrast how the ion is handled in different environments, and
> be able to defend your choices.
>
> Bill
>
> On 2/11/19 11:22 PM, Sunita Patel wrote:
>> Dear Amber users,
>> I am trying to simulate a calcium binding protein with bound calcium.
>> ff99SB force field am using for that. At the first step itself, am getting
>> following error. Although, I specified the correct atom type for calcium
>> ions, still it is unable to recognize it.
>>
>> Please advise how to counteract the problem. I need the solution urgently.
>>
>> Please help me. Thanks for the help.
>>
>> With best regards,
>> Sunita
>>
>>
>> ===================
>> WARNING: The unperturbed charge of the unit: -2.000000 is not zero.
>> FATAL: Atom .R<Ca 92>.A<C0 1> does not have a type.
>> FATAL: Atom .R<Ca 93>.A<C0 1> does not have a type.
>> Failed to generate parameters
>> Parameter file was not saved.
>> Quit
>> ===================
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Feb 12 2019 - 00:00:03 PST
