[modeller_usage] DNA nucleotide protein modeling

Dear Modeller Users

I want to model my receptor protein with single nucleotide probes. For exp: receptor ARG residue has interaction with adenine e, So I want to keep adenine in close proximity to receptor ARG.

We have done the same thing for receptor against single residue probe (mean single aa residues e.i ALA LYS or ARG residues)

But now we want to do this with a single nucleotide probe. In the case of protein, we tried this to generate a PIR file.

here is the files

>P1;PROBE_PLUS_RECEPTOR
sequence:none::.::.::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMRKQE/RKP* #RKP mean arginine lysine proline etc nut we choose only middle one K

>P1;REC # here we have receptor structure sequence
structureX:rec.reformat.pdb:FIRST: :LAST: ::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMRKQE/---* #here we have receptor with blank probes --- (for three residues)
>P1;CENTER_RES #here we choose middle residue structure while our receptor is --------------
structureX:temp_centerRes_full.pdb:FIRST: :LAST: ::::
--------------------------------------/-K-*

__________________________________Modeller script___________________________________________

# Comparative modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
from modeller.scripts import complete_pdb

log.verbose() # request verbose output

env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

mdl=complete_pdb(env,'temp_centerRes_reduced.pdb') # fill rest of residue from 2 given atoms
mdl.write('temp_centerRes_full.pdb', model_format='PDB')

# selected atoms do not feel the neighborhood
#env.edat.nonbonded_sel_atoms = 2
env.io.hetatm = True
a = automodel(env,
alnfile = 'temp_alignment.ali', # alignment filename
knowns = ('CENTER_RES', 'REC'), # codes of the templates
sequence = 'PROBE_PLUS_RECEPTOR') # code of the target

a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
a.make(exit_stage=2) # do the actual comparative modeling, exit w/o optimization

# output: pdbfile PROBE_PLUS_RECEPTOR.ini

____________________________________________________________________________

This same script also work fine for RNA nucleotides here are the results

>P1;PROBE_PLUS_RECEPTOR
sequence:none::.::.::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/g*
>P1;REC
structureX:rec.reformat.pdb:FIRST: :LAST: ::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/-*
>P1;CENTER_RES
structureX:temp_centerRes_full.pdb:FIRST: :LAST: ::::
----------------------------------------------------------/g*

script is this

# Comparative modeling by the automodel class
from modeller import * # Load standard Modeller classes
from modeller.automodel import * # Load the automodel class
from modeller.scripts import complete_pdb

log.verbose() # request verbose output

env = environ() # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.']
env.libs.topology.read(file='$(LIB)/top_heav.lib')
env.libs.parameters.read(file='$(LIB)/par.lib')

mdl=complete_pdb(env,'temp_centerRes_reduced.pdb') # fill rest of residue from 2 given atoms
mdl.write('temp_centerRes_full.pdb', model_format='PDB')

# selected atoms do not feel the neighborhood
#env.edat.nonbonded_sel_atoms = 2

a = automodel(env,
alnfile = 'temp_alignment.ali', # alignment filename
knowns = ('CENTER_RES', 'REC'), # codes of the templates
sequence = 'PROBE_PLUS_RECEPTOR') # code of the target

a.starting_model= 1 # index of the first model
a.ending_model = 1 # index of the last model
a.make(exit_stage=2) # do the actual comparative modeling, exit w/o optimization

# output: pdbfile PROBE_PLUS_RECEPTOR.ini

I used naming for RNA nucleotides are GUA CYT THY ADE

see the final model in attachment this works fine for RNA nucleotides

//////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////

I apply same thing again with DNA Nucleotides its gives me error, I used following names for DNA Resi DADE DGUA DCYT DTHY # I also want to ask is this right to use DADE DCYT etc or modeller recognise these namings DT, DA, DG, DC

here is alignment

>P1;PROBE_PLUS_RECEPTOR
sequence:none::.::.::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/l*
>P1;REC
structureX:rec.reformat.pdb:FIRST: :LAST: ::::
RYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQE/-*
>P1;CENTER_RES
structureX:temp_centerRes_full.pdb:FIRST: :LAST: ::::
----------------------------------------------------------/l*

modeller script is same as i pasted above

error is this

Read the alignment from file : temp_alignment.ali
Total number of alignment positions: 59

# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 CENTER_RE 1 1 temp_center
2 REC 58 1 rec.reforma
3 PROBE_PLU 59 2 none
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open temp_centerRes_full.pdb

Dynamically allocated memory at amaxcoordinates [B,KiB,MiB]: 495379 483.769 0.472

Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 495379 483.769 0.472
read_te_291E> Sequence difference between alignment and pdb :
x (mismatch at alignment position 1)
Alignment l
PDB .
Match
Alignment residue type 50 (l, DGUA) does not match pdb
residue type 67 (., DGU),
for align code CENTER_RES (atom file temp_centerRes_full.pdb), pdb residue number "1", chain ""

Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.

Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 CENTER_RES

Please guide thanks RNA nucleotide model is attached.

Best

ray