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Parametrizing a new residue topology file entry

Parametrizing a new residue topology file entry. Using charmm22 force field. resources. Lecture from the “hands-on” workshop in uiuc (day 06: “ Force Fields for MD simulations ”) NAMD tutorial “introducing a novel residue” NAMD tutorial “topology file tutorial”.

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Parametrizing a new residue topology file entry

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  1. Parametrizing a new residuetopology file entry Using charmm22 force field

  2. resources • Lecture from the “hands-on” workshop in uiuc (day 06: “Force Fields for MD simulations”) • NAMD tutorial “introducing a novel residue” • NAMD tutorial “topology file tutorial”

  3. When introducing a new residue • Add entry in topology file (“top_all27_prot_lipid.inp”) • Add parameters in parameter file (“par_all27_prot_lipid.inp”)

  4. Sample top file entry (Ala) name charge Group (atoms /w total charge of 0) Atom name type charge List of bonds by pairs (lines don’t matter) Hb-ignored No need for ‘double’ Improper bonds to maintain planarity- chiral atom in the middle Internal Coordinates

  5. Dividing atoms into charge groups step 1: see how original groups are defined. The GFP cro’ is composed out of 3 AA residues that cyclize (ser-tyr-gly) Missing atom

  6. Step 2: write all charges provided by new force field * * * * * * * * * * * * * * * * * * * * * Charge different than in AA entry

  7. Step 3: groups that didn’t change charge (or not specified in new ff) stay as groups, the others should be regrouped. In this case- new groups had been assigned by ff. * * * * * * * * * * * * * * * * * * * * New group

  8. Step 4: assign new groups by finding most similar group from existing ff * * * * * * * * * * * * * * * * * * * * GLN

  9. Step 5: write down all groups with sum of charges to make sure they all sum to 0

  10. Step 6: assign atom types If appears in new ff- change. Check if name changed. Original type HA C CT2 CT1 NH1 NH1 C

  11. Step 7: assign atom types to residues that didn’t change in both bonds & charges. Types from topology file. BOLD ENTRIES

  12. Step 8: assign atom types to resides that changed but don’t appear in ff According to group/charge assigned previousely GLN

  13. Step 9: summarize all atom entries

  14. Step 10: verify that all atom types defined exist in topology file. If there are atoms that don’t appear in top’ file, add it. Here ‘HA1’ is a new atom type that was added by the ff developers.

  15. Done!

  16. Improper angles • Around an sp2 center which is usually flat • In Asp the plane around CG is flat, the improper angle will be written: • IMPR CG CB OD1 OD2 • When the plane is flat- there is no relevance to order of atoms (except for central one which should be written first)

  17. Rules for impr entry • 2 impr that create the peptide bond: • (N)-(C-)-(CA)-(HN) • (C)-(CA)-(N+)-(O) • Each sp2 center is an impr center • If center isn’t flat- 2 entries • For non flat center several types:

  18. Assign impr entry to non-flat center ASN (ND2)-(CG)-(HD21)-(HD22) (ND2)-(CG)-(HD22)-(HD21) (CG)-(ND2)-(CB)-(OD1) (CG)-(CB)-(ND2)-(OD1) If 2 free atoms- put them last (HD21, HD22) & switch between them If 1 free atom- put it last (OD1) & switch between middle atoms

  19. Internal Coordinates • 2 ways to assign IC: • If all atoms are provided in the pdb file- there is no need for IC, but usually needed to complete H atoms • # IC = # atoms

  20. Rules for building IC • # IC = # atoms • All bonds must be included • Each sp2 gets to be chiral center once • Each sp3 gets to be chiral twice • Each proper dihedral is represented once (2 central atoms) • Around sp2 atom- define only 2 angles • Around sp3- define only 3 angles • Around sp (SH, OH)- define only 1 angle • In order to keep 3 angle rule for sp2- make 2 chiral entry similar in first 3 & change only last atom (example: CB-CD2-CG*-CD1, CB-CD2-CG*-CD1) • For a CH3 group, define: HD13-CG-CD1-HD11, HD13-CG-CD1-HD12 so that all 3 distances will be defined in the entry • The above is true for every C with 3 atoms connected to it • For a chiral center entry- place in 1st & 4rth place the 2 atoms for which you wish to define a bond to

  21. IC for protein backbone • Always built the same way: • -C CA N* HN • N C CA* HA • N C CA* CB • CA +N C* O • -C N CA C • N CA C +N • CA C +N +CA

  22. Step by step guide for writing IC coordinates for a residue (GLN) Step 1 take structure from top file, write down all atoms- # atoms = # IC

  23. Step 2 List all chiral centers- these are all sp3 & sp2 atoms (usually carbons) in the 3rd spot. For sp3 there are 2 entries, for sp2 there is 1. Write atom name with *

  24. Step 3 In all spots left- write all bonds between chiral centers (in spots 2 & 3). This time don’t write atom names with *. Last entry is always a bond with N+, the next N.

  25. Step 4 Fill in all the chiral entries according to the rules. Mark each bond which was defined & write down all angles. (CA)-(N)-(HN) (CA)-(N)-(C-) (CG)-(CD)-(OE1) (CG)-(CD)-(NE2) (C)-(CA)-(HA) (C)-(CA)-(CB) (C)-(CA)-(N) (CD)-(NE2)-(HE21) (CD)-(NE2)-(HE22) (N+)-(C)-(O) (N+)-(C)-(CA) (CA)-(CB)-(HB1) (CA)-(CB)-(HB2) (CA)-(CB)-(CG) (CB)-(CG)-(HG1) (CB)-(CG)-(HG2) (CB)-(CG)-(CD)

  26. Step 5 Complete regular entries by trying to walk straight lines. Check all angles defined & see if a new angle exceeds # of allowed angles. If so- define entry by different way. (CA)-(N)-(HN) (CA)-(N)-(C-) (CG)-(CD)-(OE1) (CG)-(CD)-(NE2) (C)-(CA)-(HA) (C)-(CA)-(CB) (C)-(CA)-(N) (CD)-(NE2)-(HE21) (CD)-(NE2)-(HE22) (C)-(N+)-(CA+) (N+)-(C)-(O) (N+)-(C)-(CA) (CA)-(CB)-(HB1) (CA)-(CB)-(HB2) (CA)-(CB)-(CG) (CB)-(CG)-(HG1) (CB)-(CG)-(HG2) (CB)-(CG)-(CD) EXISITING ANGLES NEW ANGLES

  27. IC coor’ assignment done Step 6: Assigning values to the coordinates. Start by measuring all distances. Start from pdb entry of residue (xyz) & measure the distances. For each distance measured, see if the specific bond exists somewhere else. For bonds of atoms that don’t exist, put an average value of this kind of bond from the literature. Next page…

  28. Pdb entry Step 6 IC distances * Distances to +/- atoms

  29. Step 7: The distances to the +/- atoms can be measured manually by opening the structure in vmd

  30. Step 8: Measure angles manually from pdb file in vmd

  31. Step 9: Measure dihedrals manually from pdb file in vmd

  32. Step 10: Measure impropers* manually from pdb file in vmd * Next page- how to measure improper angle

  33. Measuring impropers: Exactly as measuring dihedral angle. 4 atoms- a-b-c-d. Example: for the entry: CG CA2 CB2* HB21 (gfpcro’) the atoms to be marked are shown in order. Most angles in gfpcro’ are ~+,-180 4 * 3 1 2

  34. DONE!

  35. DsRedchro’ topolgy entry

  36. Angles dsredcro’ IC (C1)-(CA1)-(CB1) (C1)-(CA1)-(N1) (C2)-(CA2)-(CB2) (C2)-(CA2)-(N2) (CB2)-(CG2)-(CD1) (CB2)-(CG2)-(CD2) (C-)-(N1)-(CA1) (CZ)-(OH)-(HH) (CA1)-(CB1)-(HB11) (CA1)-(CB1)-(HB12) (CA1)-(CB1)-(CG1) (N3)-(C2)-(O2) (N3)-(C2)-(CA2) (CG2)-(CD1)-(HD1) (CG2)-(CD1)-(CE1) (C1)-(N2)-(CA2) (C1)-(N3)-(CA3) (C1)-(N3)-(C2) (CG2)-(CD2)-(HD2) (CG2)-(CD2)-(CE2) (C)-(N+)-(CA+) (CB1)-(CG1)-(HG11) (CB1)-(CG1)-(HG12) (CB1)-(CG1)-(CD3) (N3)-(CA3)-(HA31) (N3)-(CA3)-(HA32) (N3)-(CA3)-(C) (CD1)-(CE1)-(HE1) (CD1)-(CE1)-(CZ) (CG1)-(CD3)-(OE1) (CG1)-(CD3)-(NE1) (CD2)-(CE2)-(HE2) (CD2)-(CE2)-(CZ) (CA3)-(C)-(O) (CA3)-(C)-(N+) (CD3)-(NE1)-(HE12) (CD3)-(NE1)-(HE11) (CE2)-(CZ)-(OH) (CE2)-(CZ)-(CE1) (CA2)-(CB2)-(HB2) (CA2)-(CB2)-(CG2) (CA1)-(C1)-(N2) (CA1)-(C1)-(N3)

  37. GFP chro’ topolgy entry Atom names taken from pdb 1WUR H atoms included in pdb file

  38. Angles gfpcro’ (C-)-(N1)-(HN11) (C-)-(N1)-(CA1) (CA3)-(C3)-(O3) (CA3)-(C3)-(N+) (CE2)-(CZ)-(OH) (CE2)-(CZ)-(CE1) (C2)-(CA2)-(CB2) (C2)-(CA2)-(N2) (N1)-(CA1)-(HA1) (N1)-(CA1)-(CB1) (N1)-(CA1)-(C1) (CB1)-(OG2)-(HOG) (C3)-(N+)-(CA+) (CA2)-(CB2)-(HB21) (CA2)-(CB2)-(CG) (CZ)-(OH)-(HO (CA1)-(CB1)-(HB11) (CA1)-(CB1)-(HB12) (CA1)-(CB1)-(OG2) (C1)-(N2)-(CA2) (CB2)-(CG)-(CD1) (CB2)-(CG)-(CD2) (CA1)-(C1)-(N2) (CA1)-(C1)-(N3) (CG)-(CD1)-(HD1) (CG)-(CD1)-(CE1) (C1)-(N3)-(C2) (C1)-(N3)-(CA3) (CG)-(CD2)-(HD2) (CG)-(CD2)-(CE2) (N3)-(C2)-(O2) (N3)-(C2)-(CA2) (CD1)-(CE1)-(HE1) (CD1)-(CE1)-(CZ) (N3)-(CA3)-(HA31) (N3)-(CA3)-(HA32) (N3)-(CA3)-(C3) (CD2)-(CE2)-(HE2) (CD2)-(CE2)-(CZ)

  39. GFP cro’ IC entry

  40. GFP cro’ IMPR entry Not sure about N3 being a chiral center

  41. GFP cro’ atom entry

  42. GFP bond entry

  43. Summary- adding a topology entry • Have a pdb file, list atoms & draw • Divide atoms into groups of 0 charges (some atoms & charges taken from new FF) • List all bonds in molecule • Impr • Assign IC & measure values • Write entry. Use format from existing entry • Pick a name for residue • Add to existing topology file

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