Re: psfgen error protein-ligand

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Fri Oct 04 2019 - 10:29:39 CDT

Dear Pavel,

 

The residue and atoms’ names of the pdb and topology file have to match. When renaming the atoms, please make sure that they correspond. But, what do you mean that the docking pose is lost? Psfgen have only two ways to get the coordinates, from the pdb that you loaded, or from the IC cards. If the names of the pdb match the topology, it should not be using the IC cards.

 

If the hydrogen atoms are not present in the pdb, and their coordinates are guessed, that message is printed. This guess is purely geometry-based. 

 

Best,

 

João

 

 

From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Pavel Kostadinov <pkcre_at_abv.bg>
Reply-To: <namd-l_at_ks.uiuc.edu>, Pavel Kostadinov <pkcre_at_abv.bg>
Date: Friday, October 4, 2019 at 2:46 AM
To: <namd-l_at_ks.uiuc.edu>
Subject: namd-l: psfgen error protein-ligand

 

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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