From: Pavel Kostadinov (pkcre_at_abv.bg)
Date: Fri Oct 04 2019 - 02:42:08 CDT
Dear NAMD users, 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 (from C,O,N to C1,O2,N1 - the way I find them in the .str file) since they might not be CHARMM appropriate. On doing that, however, the correct docking pose is lost, 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? Thank you in advance, I appreciate your willingness to help! Greetings, Pavel.
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