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
--
Sergio Garay
Dr. en Ciencias Biológicas
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221