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Non-standard residue definitions

Generalities


For handling non-standard atoms and residues like ions or ligands the user has to modify several of the CNS specific scripts and definition files. Usually the CNS script "generate.inp" is executed for generating a PSF file. This has to be patched manually and copied to the cns/protocols directory of the run's local directory tree if one wants to setup the PSF file in the ARIA run.

Instead of modifying the "generate.inp" script, one could copy the PSF and the "_template" PDB file to the "cns/begin" directory and disable the generation of these files via the GUI (node "CNS" in the "Structure Generation" sub-tree or the project tree). Also the definition files for methyl groups ("methyls.tbl") and of prochiral groups ("setup_swap_list.tbl"), located in the same directory, should be checked manually.

Additionally topology, parameter and linkage files have to be modified. Make sure that you introduce the right bonds if you want to use torsion angle dynamics in the structure generation. User-specific files can be set via the GUI in the "Sequence" panel.

The Hetero-compound Information Centre might assist you in creating the necessary patches and modifications in the definition files.



An example of introducing modified residues



To help you to set-up your own example, here the description of a project on a peptide containing modified residues. This example was provided by Hélène Déméné and Gaetan Bellot, from Centre de Biochimie Structurale (Montpellier, France). The full example is described in the Tutorials folder, and only the data related to the chemical modifications are presented in this page.

The example presents the study of a cyclic peptide interacting with G protein-coupled receptors (GPCRs), and more details about the corresponding research can be found on the page of Hélène Déméne.


The peptide sequence, shown below, contains 4 modified amino-acids: GLX (chiral D Glutamine), NLE (Norleucine), GLI (Glycine before cyclisation) and CYC (cyclisated Cysteine).

GLIGLX
VAL
LEU
ILE
PHE
ARG
GLU
ILEHIS
ALA
SER
LEU
VAL
PRO
GLY
PRO
SER
GLU
ALA
GLYARGARG
ARGARGGLYARGARGTHRGLYSERPROSERGLUGLYALAHISVALSERALA
ALANLEALA
LYSTHRVALARGNLETHRCYC











The following files have to be modified:

  • CNS files contained in the cns/toppar directory (in the ARIA distribution as well as in the run):
    • topology libraries: topalldg5.3.pro and topalldg.5.3.pep
    • parameter files parall* may have to be modified, in case of the introduction of new atom, types, or new potential terms.
  • ARIA files:
    • in the directory src/py/data of the ARIA distribution: atomnames.xml and iupac.xml
    • in the directory src/py/legacy of the ARIA distribution: PseudoAtom.py, Nomenclature.py and AminoAcid.py

CNS Files


In the file topallhdg5.3.pro, the residues GLX, NLE, GLI and CYC were added:

Residue GLX
residue GLX  
group
atom N    type=NH1 charge=-0.36 end
atom HN   type=H   charge= 0.26 end
atom CA   type=CH1E  charge= 0.00 end
atom HA   type=HA  charge= 0.10 end
atom CB   type=CH2E  charge=-0.20 end
atom HB1  type=HA  charge= 0.10 end
atom HB2  type=HA  charge= 0.10 end
atom CG   type=CH2E  charge=-0.20 end
atom HG1  type=HA  charge= 0.10 end
atom HG2  type=HA  charge= 0.10 end
atom CD   type=C   charge= 0.48 end
atom OE1  type=O   charge=-0.48 end
atom NE2  type=NH2 charge=-0.52 end
atom HE21 type=H   charge= 0.26 end
atom HE22 type=H   charge= 0.26 end
atom C    type=C   charge= 0.48 end
atom O    type=O   charge=-0.48 end

bond N  HN
bond N  CA     bond CA  HA
bond CA CB     bond CB  HB1     bond CB  HB2
bond CB CG     bond CG  HG1     bond CG  HG2
bond CG CD
bond CD OE1
bond CD NE2    bond NE2 HE21    bond NE2 HE22
bond CA C
bond C  O

improper HA C N CB 
improper CD  CG OE1  NE2
improper NE2 CD HE21 HE22
improper CG  CD NE2  HE21
improper HB1 HB2 CA CG 
improper HG1 HG2 CB CD 

dihedral CG  CB  CA  N
dihedral CD  CG  CB  CA
dihedral OE1 CD  CG  CB
end
                                                                                                                                                   
Residue NLE

residue NLE
group
atom N   type=NH1 charge=-0.360 end
atom HN  type=H   charge= 0.260 end
atom CA  type=CH1E  charge= 0.000 end
atom HA  type=HA  charge= 0.100 end
atom CB  type=CH2E  charge=-0.200 end
atom HB1 type=HA  charge= 0.100 end
atom HB2 type=HA  charge= 0.100 end
atom CG  type=CH2E  charge=-0.200 end
atom HG1 type=HA  charge= 0.100 end
atom HG2 type=HA  charge= 0.100 end
atom CD  type=CH2E  charge=-0.200 end
atom HD1 type=HA  charge= 0.100 end
atom HD2 type=HA  charge= 0.100 end
atom CE  type=CH3E  charge=-0.200 end
atom HE1 type=HA  charge= 0.100 end
atom HE2 type=HA  charge= 0.100 end
atom HE3 type=HA  charge= 0.100 end
atom C  type=C   charge= 0.480 end
atom O   type=O   charge=-0.480 end

bond N  HN
bond N  CA     bond CA HA
bond CA CB     bond CB HB1     bond CB HB2
bond CB CG     bond CG HG1     bond CG HG2
bond CG CD     bond CD HD1     bond CD HD2
bond CD CE     bond CE HE1     bond CE HE2 bond CE HE3
bond CA C
bond C  O

improper HA N C CB
improper HB1 HB2 CA CG 
improper HG1 HG2 CB CD
improper HD1 HD2 CG CE 
improper HE1 HE2 CD HE3 

dihedral CG  CB  CA  N
dihedral CD  CG  CB  CA
dihedral CE  CD  CG  CB

end
                                                                                                                                                

Residue GLI
residue GLI 
group
atom N type=NH1 charge=-0.570 end
atom HN type=H charge= 0.370 end
atom CA type=CH2G charge= 0.200 end
atom HA1 type=HA charge= 0.000 end
atom HA2 type=HA charge= 0.000 end
atom C type=C charge= 0.500 end
atom O type=O charge=-0.500 end

bond N HN
bond N CA bond CA HA1 bond CA HA2
bond CA C
bond C O

DONO HN N
ACCE O C

improper HA1 HA2 N C
end


Residue CYC

residue CYC  
group
atom N   type=NH1 charge=-0.36 end
atom HN  type=H   charge= 0.26 end
atom CA  type=CH1E  charge= 0.00 end
atom HA  type=HA  charge= 0.10 end
atom CB  type=CH2E  charge=-0.20 end
atom HB1 type=HA  charge= 0.10 end
atom HB2 type=HA  charge= 0.10 end
atom CG  type=CH2E  charge=-0.20 end
atom HG1 type=HA  charge= 0.10 end
atom HG2 type=HA  charge= 0.10 end
atom SG  type=SM   charge=-0.14 end
atom CD  type=C   charge= 0.48 end
atom OE1  type=O   charge=-0.48 end
atom NE2  type=NH2 charge=-0.52 end
atom HE21 type=H   charge= 0.26 end
atom HE22 type=H   charge= 0.26 end
atom OC  type=O   charge=-0.29 end
atom C   type=C   charge= 0.48 end

bond N  HN
bond N  CA     bond CA HA
bond CA CB     bond CB HB1     bond CB HB2
bond CB SG     bond SG CG     bond CG HG1 bond CG HG2
bond CG CD     bond CD OC
bond C OE1
bond C NE2     bond NE2 HE21    bond NE2 HE22
bond CA C

improper HA N C CB 
improper HB1 HB2 CA SG
improper CG SG HG1 HG2
improper C  CA OE1  NE2
improper NE2 C HE21 HE22
improper CA C  NE2  HE21

angle CB SG CG
angle SG CG CD
dihedral SG CB CA N
dihedral CA CB SG CG
dihedral CB SG CG CD
dihedral SG CB CA C
dihedral SG CG CD OC
dihedral OE1 C CA CB

end

                                                                                                                                                   
An additional residue PEPC  is used for the peptide cyclisation:

PRESidue PEPC

ADD BOND -CD +N
ADD ANGLE -CG -CD +N
ADD ANGLE -OC -CD +N
ADD ANGLE -CD +N +CA
ADD ANGLE -CD +N +HN

ADD DIHEdral -SG -CG -CD +N
ADD DIHEdral -CG -CD +N +CA

ADD IMPRoper -CG -CD +N +HN
ADD IMPRoper  -OC -CD +N +CA 
ADD IMPRoper -CG -CD +N +CA 

end

                                                                                                                                                   

File topallhdg5.3.pep


The definition of residues allowed at the Cterm and Nterm places is modified, because CYC can be N-terminal only, and GLI C-terminal only.


first PROP            tail + PRO   end

first NTER            tail + ALA   end
first NTER            tail + ARG   end
first NTER            tail + ASN   end
first NTER            tail + ASP   end
first NTER            tail + CYS   end
first NTER            tail + GLN   end
first NTER            tail + GLU   end
first NTER            tail + GLY   end
first NTER            tail + HIS   end
first NTER            tail + ILE   end
first NTER            tail + LEU   end
first NTER            tail + LYS   end
first NTER            tail + MET   end
first NTER            tail + PHE   end
first NTER            tail + PRO   end
first NTER            tail + SER   end
first NTER            tail + THR   end
first NTER            tail + TRP   end
first NTER            tail + TYR   end
first NTER            tail + VAL   end
first NTER            tail + GLX   end
first NTER            tail + NLE   end
first NTER            tail + CYC   end

last  CTER head - ALA              end
last  CTER head - ARG              end
last  CTER head - ASN              end
last  CTER head - ASP              end
last  CTER head - CYS              end
last  CTER head - GLN              end
last  CTER head - GLU              end
last  CTER head - GLY              end
last  CTER head - HIS              end
last  CTER head - ILE              end
last  CTER head - LEU              end
last  CTER head - LYS              end
last  CTER head - MET              end
last  CTER head - PHE              end
last  CTER head - PRO              end
last  CTER head - SER              end
last  CTER head - THR              end
last  CTER head - TRP              end
last  CTER head - TYR              end
last  CTER head - VAL              end
last  CTER head - GLX              end
last  CTER head - NLE              end
last  CTER head - GLI              end


ARIA Files


The following files have to be modified in order to include the modified residues:

  • src/py/data/atomnames.xml: contains the atom names of all possible residues. see the file
  • src/py/data/iupac.xml: IUPAC atom names. see the file
  • src/py/legacy/PseudoAtom.py: Definition of pseudo atoms. see the file
  • src/py/legacy/Nomenclature.py: rules for converting atom names and definitions of methylene and methyl groups. see the file
  • src/py/legacy/AminoAcid.py: rules for converting residue names (one-letter and three-letter codes). see the file

An example of run with thecyclic peptide presented here, is available in the tutorial page Modified residues.

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