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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>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Tue Jun 05 2012 - 11:30:03 PDT
