Re: psfgen error protein-ligand

From: Pavel Kostadinov (pkcre_at_abv.bg)
Date: Sat Oct 05 2019 - 11:17:07 CDT

Dear João,
  Thank you for your reply. To me, the problem seems to come from the pdb file. This is how to correct docking pose looks like:
https://photos.app.goo.gl/qbjvP1JNAvpyyM249
  My pdb file looks like this: ... ATOM
 
4634
 C
 
GLY A 584
 
 
 18.684
 
9.185
 49.432
 1.00130.85
 
 
 
 
 
C

  ATOM
 
4635
 O
 
GLY A 584
 
 
 19.885
 
8.917
 49.405
 1.00125.62
 
 
 
 
 
O
 
 
  TER HETATM 4636
 O
 
UNK
 
 
0
 
 
 14.107
 -5.022
 28.492
 0.00
 0.00
 
 
 
 
 
O

  HETATM 4637
 C
 
UNK
 
 
0
 
 
 12.656
 -5.392
 28.849
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4638
 N
 
UNK
 
 
0
 
 
 11.204
 -5.762
 29.207
 0.00
 0.00
 
 
 
 
 
N

  HETATM 4639
 C
 
UNK
 
 
0
 
 
 10.910
 -6.594
 30.468
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4640
 C
 
UNK
 
 
0
 
 
 11.184
 -8.110
 30.471
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4641
 C
 
UNK
 
 
0
 
 
 11.647
 -8.812
 29.181
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4642
 C
 
UNK
 
 
0
 
 
 13.133
 -9.165
 28.988
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4643
 C
 
UNK
 
 
0
 
 
 13.780
 -9.037
 27.596
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4644
 C
 
UNK
 
 
0
 
 
 14.996
 -8.114
 27.393
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4645
 N
 
UNK
 
 
0
 
 
 16.316
 -8.688
 26.848
 0.00
 0.00
 
 
 
 
 
N

  HETATM 4646
 C
 
UNK
 
 
0
 
 
 17.653
 -8.309
 27.513
 0.00
 0.00
 
 
 
 
 
C

  HETATM 4647
 O
 
UNK
 
 
0
 
 
 18.990
 -7.931
 28.178
 0.00
 0.00
 
 
 
 
 
O

  CONECT 4636 4637 CONECT 4637 4636 4638 CONECT 4638 4637 4639 CONECT 4639 4638 4640 CONECT 4640 4639 4641 CONECT 4641 4640 4642 CONECT 4642 4641 4643 CONECT 4643 4642 4644 CONECT 4644 4643 4645 CONECT 4645 4644 4646 CONECT 4646 4645 4647 CONECT 4647 4646
  END
When I try to change the 3rd row with the HETATM names (in which case the psfgen seems to work) with the names as I see them in the .str file from CGenFF, the docking pose is lost. The wrong docking pose looks like this:
https://photos.app.goo.gl/eWnGVMgt2xV4urA49
  It seems rather illogical to me why this would happen, I`m not changing any of the numbering of the pdb file, just the atom names, and the docking pose is lost somehow (I can see it the moment I load the molecule into VMD). How do you explain this to yourself? Why by altering this column VMD does not recognize the right topology of the ligand?
  Best regards, Pavel.

>-------- Оригинално писмо --------

>От: Joao Ribeiro jribeiro_at_ks.uiuc.edu

>Относно: Re: namd-l: psfgen error protein-ligand

>До: , Pavel Kostadinov

>Изпратено на: 04.10.2019 18:29

 
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    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: on behalf of Pavel Kostadinov
 Reply-To: , Pavel Kostadinov
 Date: Friday, October 4, 2019 at 2:46 AM
 To:
 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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