On Fri, Apr 01, 2016, Martina Devi wrote:
>
> I used the given command to create a hoogsten base pair for Guanine but the
> pdb which is generated does not have the hoogsten base pair but shows a
> watson crick base pair. Though the pdb gets generated it shows
>
> title:
> default_name
> useboundsfrom: atom mismatch:m1(13) & m2(0)
> useboundsfrom set bounds for 0 atoms
>
> May I know if there is any mistake with the input.
>
> molecule m;
> bounds b;
>
> m = fd_helix( "arna", "g", "rna");
> b = newbounds ( m, "ag.1X.pdb");
>
> useboundsfrom(b, m, "1:1,5:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ag.IX.pdb"),"::,H?[
> T]",0.1);
> useboundsfrom(b, m, "1:2,6:??,H?
> T]",getpdb("/root/home/Amber12/amber12/dat/dgdb/basepairs/ga.IX.pdb"),"::,H?[
> T]",0.1);
>
> putpdb( "b.pdb", m, "-wwpdb");
As the message says, there is some mismatch in your atom expressions. But
fixing that alone won't help: the useboundsfrom() command is something
you do in advance of carrying out distance geometry. Just setting up the
bounds matrix doesn't do anything to the coordinates: you have to embed
and refine the structures as well.
To debug the atom expressions, try something like this:
atom a;
string aexpr;
aexpr = "...something you want to test....";
for (a in m){
if( a =~ aexpr) printf( "%s\n", a.fullname );
}
That will print out the atoms that match--make sure you are getting what you
want.
...good luck....dac
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Received on Fri Apr 01 2016 - 10:00:03 PDT
