Jonathan,
the syntax for addions command is as follows: addions <model_name> <ion>
<number of ions>
The last argument is the number of ions you wish to add, not the desired
total charge.
In your case, the command will be: addions pdb Na+ 3
Hope it helps
Sasha
On 9/11/2012 11:03 AM, Carmenza Martinez wrote:
> one simple question...do you absolutely need to add ions? Sometimes adding
> ions can be troublesome and cause instability to the simulation. Are you
> only doing it just to make sure that the "unperturbed charge of the unit"
> is zero? or is it something that your simulation must have in order to
> answer your question...
>
>
> On Tue, Sep 11, 2012 at 1:43 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
>> I'm having trouble adding ions.
>>
>> Here is what I did
>>
>> edited pdb.
>> loaded into xleap (leap added a missing atom and H's)
>> saveoff .lib
>> saveoff .pdb
>> saveamberparm pdb .prmtop .inpcrd
>>
>> and I get:
>>
>> WARNING: The unperturbed charge of the unit: -3.000000 is not zero.
>>
>> (files were created)
>>
>> therefore I tried adions pdb Na+ 0
>> (argument #1 is a type string unit)
>>
>> am1=createUnit pdb
>>
>> addions am1 Na+ 0
>> Na+ has a charge of 0.
>> addIons: Can't neutralize.
>>
>> from what i understand I created a unit and tried to neutralize, but... no
>> bueno. The endgame is to do a simple minimization of this protein.
>> any suggestions on how to get un-stuck?
>>
>> Thanks and sorry for the simplicity of the question. I did search the
>> archives and tutorials, but I'm a bit lost. I'm missing something simple.
>>
>> Jonathan
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Sep 11 2012 - 11:30:05 PDT
