I have been trying to run psfgen for a protein in question (albumin) and a ligand (diisocyanate) from a docking pose. I have parameterized my ligand with CGenFF and downloaded the CHARMM topology and parameter files required for the psfgen run. However, on running the plug-in I obtained a warning that psfgen failed to set coordinates for the atoms:
psfgen) Warning: failed to set coordinate for atom O UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom N UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom N UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom C UNK:0 XO1 psfgen) Warning: failed to set coordinate for atom O UNK:0 XO1
Then I decided to change the names of the heteroatoms in the .pdb file (HDI414.pdb) since they might not be CHARMM appropriate. On doing that, however, the correct docking pose is lost (wrong.docking.pose.png), BUT!!! I managed to create .psf file for this wrong pose. Still, I receive warning that coordinates for hydrogen atoms, which are not included in the pdb, are poorly guessed.
psfgen) Warning: poorly guessed coordinate for atom H1 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H2 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H3 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H4 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H5 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H6 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H7 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H8 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H9 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H10 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H11 UNK:0 XO1 psfgen) Warning: poorly guessed coordinate for atom H12 UNK:0 XO1
I have tried many things: from writing separate .str files from the one I obtained from CGenFF to changing the residue names in the pdb file, but nothing seems to work. How to change the pdb file in such a way so I don't lose my docking pose and the CHARMM files (and NAMD) recognize the ligand? I have uploaded pngs of the docking poses, my CGenFF .str file and the altered .pdb, I hope it helps.
Thank you in advance, I appreciate your willingness to help!
Greetings,
i use neither VMD's psfgen nor CHARMM force field but:
1.Align the x, y, and z coordinates of the ligand with the x, y, and z coordinates of the protein to recover the "correct" pose.
2. Assuming that the ligand is already defined in the library, make sure that the ligand name and all atom names of the ligand in the PDB file correspond to the library.
Questions: Why is the ligand without the hydrogens? How did you obtain partial atomic charges of the ligand (without the hydrogens)? How sure are you about the identical partial atomic charges of all hydrogens?
Hi
I usually use the Protparam server to generate the topology files and parameters of the ligand.
1) Convert your ligand pose in format *.mol2 with all hydrogens using openbabel (or equivalent) program.
2) Submit file to Protparam server.
3) The generated topology file will be in the LIGAND.rtf file. In this file, rename the ligand (LIG) to the same name as the PDB.
4) In vmd, add the ligand topology and use psfgen to generate the *.psf file
5) If you want more precise force fields, replace the partial charges of atoms for more precise charges, eg CHELPG charges after MM calculations with gausian or orca programs.
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