Prepare Protein pdb file for setup utilities

% cd prot_setup

Edit vm1_prot.pdb and remove header lines and all lines after the TER line of the protein. THis will remove all other molecules as well as the header lines and conect lines.

Protonation states of Histidines

Analyze the vicinity of atoms NE2 and ND1 for the histidines in this pdb file. It shows that the most likely protonation state based on nearby H-bond candidates is ND1 protonated in all three cases.

  1. Use vmd with the pdb file vm1_prot.pdb which was extracted from 1VM1.pdb. Use the selection box to select:

    within 4 of ((resname HIS) and (name ND1 NE2))

  2. Use bond picking to get the distances
    1. choose which his to look at first, press c (center), click that his
    2. zoom in: press s (scale), press m1 while sliding to right
    3. rotate and translate to get good orientation: press r (rotate) t (translate)
    4. pick the atoms that you want the distances of: press 2 (pick bonds, you click 2 atoms per bond) click NE1, then any atom near it
  3. You will find in HIS289 that there are 2 nearby O's for NE2 and 2 nearby O's for ND1
  4. The closest to ND1 are the carbonyl O's of ALA285 and PRO27, thus I would pick the ND1 to be protonated.
  5. The NE2 is less clear so I would allow it to be unprotonated.
  6. The other two HIS's have clear proton acceptors for ND1 but nothing for NE2
  7. So all Histidines appear to be most likely HID protonation states. Edit vm1_prot.pdb and change all HIS to HID.

Disulfide Bonds

  1. First check for SSBOND entries in the original pdb file header: SSBOND 1 CYS A 77 CYS A 123
  2. Otherwise check with vmd for anythine "within 3 of resname CYS and name SG"
  3. Edit vm1_prot to change CYS to CYX for residues 77 and 123 (the only CYS's in this pdb as it turns out).
This file is now ready for leap processing.

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