Dear all,
I’m trying to find a way to construct a superhelix A-form DNA structure (or say nucleosome-like structure) with relative short basepairs (less than 100).
I know NAB can do this ($AMBERHOME/ AmberTools/examples/nab/ program_10.nab), but the tricky part is that NAB only supports to construct a nucleosome model based on B-form DNA, and what I want is to construct a nucleosome model based on A-form DNA.
1. I tried to modify the code by changing the input parameter of wc_helix() from
“m1 = wc_helix( sbase, "", "dna", abase, "", "dna", 2.25, -4.96, 0.0, 0.0, "" );”
to
“m1 = wc_helix( sbase, "", "dna", abase, "", "dna", -6.0, 20.0, 0.0, 0.0, "" );”
And I failed in getting a right A-type geometry, which is predictable, as it is mentioned in the manual that wc_helix() is not a generic method for constructing different types of helixes.
1. I then tried to replace wc_helix() function with fd_helix() function, then I got the error below:
program_10.nab:55 syntax error
nab2c failed!
I think the reason I got this information was that the molecules fd_helix() generated didn’t label with A/B strand, so the molecular fd_helix() generated can’t be used for the afterward functions like mergestr().
Since I’m not an expert in NAB language and there are very few discussions about NAB online, I’m emailing to seek your help. Any suggestions would be highly appreciated.
Best,
Qinsi
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 30 2022 - 17:00:03 PDT
