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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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resources
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”
when introducing a new residue
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”)
sample top file entry ala
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

dividing atoms into charge groups
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

slide6

Step 2: write all charges provided by new force field

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

*

* Charge different than in AA entry

slide7

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

slide10

Step 6: assign atom types

If appears in new ff- change. Check if name changed.

Original type

HA

C

CT2

CT1

NH1

NH1

C

slide11

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

BOLD ENTRIES

slide12

Step 8: assign atom types to resides that changed but don’t appear in ff

According to group/charge assigned previousely

GLN

slide14

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.

improper angles
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)
rules for impr entry
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:
assign impr entry to non flat center
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

internal coordinates
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
rules for building ic
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
ic for protein backbone
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
step by step guide for writing ic coordinates for a residue gln
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

slide23

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 *

slide24

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.

slide25

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)

slide26

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

slide27

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…

slide28

Pdb entry

Step 6 IC distances

* Distances to +/- atoms

slide29

Step 7:

The distances to the +/- atoms can be measured manually by opening the structure in vmd

slide30

Step 8:

Measure angles manually from pdb file in vmd

slide31

Step 9:

Measure dihedrals manually from pdb file in vmd

slide32

Step 10:

Measure impropers* manually from pdb file in vmd

* Next page- how to measure improper angle

slide33

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

angles dsred cro ic
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)

gfp chro topolgy entry
GFP chro’ topolgy entry

Atom names taken from pdb 1WUR

H atoms included in pdb file

angles gfp cro
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)

slide40

GFP cro’ IMPR entry

Not sure about N3 being a chiral center

summary adding a topology entry
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