Dear Modeller's Users:
I'm trying to model a protein dimer interacting with a small DNA molecule. Following the manual instructions I was able to build my dimer using:
>P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer *
But I have some problems to add my DNA molecule as an additional restraint:
I added to my script:
env.io.hetatm = True
And I also added my DNA molecule (all the DNA atoms were named HETATM) into the template pdb and modified my alignment in this way:
>P1; my_target xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / yyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyyy --> second monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) * >P1; my_template hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh --> first monomer ---------- --> alignment of extra dna residues (I'm not sure is this is right) / kkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkkk ---> second monomer ---------- --->alignment of extra dna residues (I'm not sure is this is right) / ---------------------------------------------------- ---> 1st strand of DNA ............. / ---------------------------------------------------- ---> 2nd strand of DNA ............. * Modeller worked without any warning but my dimer pass through the DNA molecule, so this is not working.
Any help would be very appreciated.
Sergio