Just remove the base, rename the rest - sugar and phosphate backbone
to a new nucleoside name and Leap or NAB should be able to rebuilt
the new base in more or less good orientation (given some small
fluctuations around the chi angle).
Piotr
> Thanks David!
>
>
> Yes, it was my mistake, I was following an example from an old version of
> the AmberTools manual and the sequence was given in lowercase letters, I
> am guessing that was the whole problem since I changed that in my input
> file and now it works perfectly. (yes, I have been using AmberTools12)
>
> About my second question. I have a nucleotide sequence I got from the PDB
> database and I need to mutate it. I need to change one of the nucleotides
> in the middle to a different one. I thought about reading the reference
> one, then create a second one with the right sequence and then do a
> "superimpose()" to try to make the created sequence to adopt a similar
> geometry as the reference one, but I am not sure if that would be the best
> way to do this.
>
>
> Thanks!
>
>
>
>> On Tue, Jun 05, 2012, Romelia Salomon wrote:
>>>
>>> I have couple questions about NAB.
>>>
>>> 1) I am trying to create a nucleotide sequence in a random
>>> configuration,
>>> I am using link_na but I get the following error
>>>
>>> Residue g not in library rna.amber94.rlb.
>>
>> This sounds like an old version of the code. Please upgrade to
>> AmberTools12,
>> if you have not already done so. If that doesn't help, you should post
>> the
>> program that has the call to link_na().
>>
>>>
>>> I also tried the example that comes in the manual "// Program 8 -
>>> create
>>> a
>>> pseudoknot using distance geometry" as it uses similar calls to the one
>>> I
>>> have and I still got the same error.
>>
>> Program 8 works for me (again in AmberTools12).
>>
>>>
>>> 2) I need to substitute a nucleotide from a sequence, what would be the
>>> best way to do it with NAB? Is
>>
>> I think we need more context here.
>>
>> ....dac
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
> --
> ****************************************
> Romelia Salomon
> Walker Group
> 398 San Diego Supercomputing Center
> UC San Diego
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jun 05 2012 - 13:30:03 PDT
