Thanks Piotr, it worked beautifully!
> 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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>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>> --
>> ****************************************
>> Romelia Salomon
>> Walker Group
>> 398 San Diego Supercomputing Center
>> UC San Diego
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
****************************************
Romelia Salomon
Walker Group
398 San Diego Supercomputing Center
UC San Diego
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Received on Tue Jun 05 2012 - 15:30:03 PDT
