Hi,
I am using NAB from AMBERTOOLS21 to connect two RNA duplexes. Here, I wish
to align sequences at common bases using "superimpose" and then connect
eventually with "connectres". I am using this as an example to test
*superimpose* and *connectres* functionalities.
NAB script (shown below) runs without error and gives rmsd 0 (suggesting
successful alignment). The problem is when I see structures in VMD
(ref_1.pdb and sup_rna.pdb) they are not aligned at all as expected.
I am expecting that fragment 2 will be on top of fragment 1 with base-pair
C:G aligned. Please advise if I am missing something here.
Please see the NAB script here:
##############
//A-form duplex
// trying to connect two fragments: Fragment 1: UUUU; Fragment 2: AUGA
// Point of alignment is common base "C" in both sequences
// Creating RNAs first
molecule m1, m2, m_ref, m_align ;
float r ; // variable r for RMSD
m1 = fd_helix( "arna", "uuuuc", "rna" );
m2 = fd_helix( "arna", "cauga", "rna" );
putpdb( "rna_1.pdb", m1);
putpdb( "rna_2.pdb", m2);
// reading PDBs and aligning
//m_ref = reference molecule
m_ref = getpdb("rna_1.pdb");
//m_align = molecule to be aligned
m_align = getpdb("rna_2.pdb");
//superimpose( m_align,"1,10,C[1-5]',O4'" , m_ref, "5,6,C[1-5]',O4'");
superimpose( m_align,"1,10" , m_ref, "5,6");
putpdb ("sup_rna.pdb", m_align);
rmsd( m_ref, "::C1'", m_align, "::C1'", r );
printf( "rmsd = %8.3fn", r );
################
Best Regards,
Mandar Kulkarni
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Received on Mon Jun 07 2021 - 15:00:02 PDT
