From: Joao Ribeiro KS (jribeiro_at_ks.uiuc.edu)
Date: Thu Apr 09 2020 - 09:20:48 CDT
Hi Marcos,
Some questions.
What do you mean by "Pre-processed the protein file with QwikMD"? The
initial PDB file should include both protein and ligand, ensuring the
continuity atoms' index numbering.
Did you try to use the CGenFF webserver? Also, when guessing the topology,
please make sure that the parameters are included in the topology file,
meaning that you need a stream file (str) rather than a topology-only file
(rtf). CGenFF server can produce this file if you select the option to
include the parameters.
I hope this helps.
Best,
Joao
On Sun, Apr 5, 2020 at 3:38 AM Marcos Verissimo Alves <
marcos_verissimo_at_id.uff.br> wrote:
> Hi all,
>
> I am trying to run a calculation by generating the input files with QwikMD
> (in vmd-1.9.4a38) with a protein plus a ligand (favipiravir) that is not
> parametrized in the original CHARMM forcefields, but I am getting an error
> when preparing the system. Basically these are the steps I took:
>
> 1 - Prepared a topology for the ligand using the SwissParam server. Since
> favipiravir is not in the SwissParam database and does not have a PDB ID, I
> replaced "LIG" in the resulting SwissParam rtf file with "CA95" (the name I
> want to give to the ligand). The RESI entry of the rtf file thus looks like
>
> DEFA FIRS NONE LAST NONE
> AUTO ANGLES DIHE
>
> RESI CA95 0.00
>
> 2 - Pre-processed the protein file with QwikMD, with no problems. Then I
> appended the ligand coordinates to the PDB file of the ligand and saved it
> as "complex.pdb". The end of my complex.pdb file is as follows:
>
> ATOM 4644 OT1 THR A 304 -4.515 -10.000 -16.867 0.00 0.00 AP1
> ATOM 4645 OT2 THR A 304 -5.888 -10.866 -15.897 0.00 0.00 AP1
> HETATM 1 C1 CA95A 500 4.473 -27.094 21.158 1.00 0.00
> AP1 C
> HETATM 2 C2 CA95A 500 4.276 -28.495 21.183 1.00 0.00
> AP1 C
> HETATM 3 N1 CA95A 500 3.071 -29.050 21.037 1.00 0.00
> AP1 N
> HETATM 4 C3 CA95A 500 2.028 -28.242 20.860 1.00 0.00
> AP1 C
> HETATM 5 C4 CA95A 500 2.231 -26.862 20.837 1.00 0.00
> AP1 C
> HETATM 6 N2 CA95A 500 3.405 -26.302 20.979 1.00 0.00
> AP1 N
> HETATM 7 H CA95A 500 6.882 -28.125 21.472 1.00 0.00 AP1
> HETATM 8 N CA95A 500 6.904 -27.114 21.456 1.00 0.00
> AP1 N
> HETATM 9 H1 CA95A 500 7.786 -26.633 21.569 1.00 0.00 AP1
> HETATM 10 C CA95A 500 5.793 -26.356 21.318 1.00 0.00
> AP1 C
> HETATM 11 O CA95A 500 5.820 -25.124 21.315 1.00 0.00
> AP1 O
> HETATM 12 O1 CA95A 500 5.318 -29.333 21.362 1.00 0.00
> AP1 O
> HETATM 13 H2 CA95A 500 4.979 -30.248 21.337 1.00 0.00 AP1
> HETATM 14 H3 CA95A 500 1.041 -28.680 20.740 1.00 0.00 AP1
> HETATM 15 F CA95A 500 1.182 -26.047 20.660 0.00 0.00
> AP1 F
>
> 3 - Loaded "complex.pdb" to QwikMD, added the CA95 topology to the
> library, restarted it and the complex was displayed correctly in the OpenGL
> display. However, when I click on "Prepare" (for a basic run), in the text
> console of VMD I see that psfgen gives me the following error:
>
> psfgen) unknown residue type CA95
> psfgen) extracted 1 residues from pdb file
> psfgen) setting patch for first residue to none
> psfgen) setting patch for last residue to none
> psfgen) Info: generating structure...psfgen) unknown residue type CA95
> failed!
>
> Am I doing something wrong or missing anything?
>
> Thanks in advance,
>
> Marcos
> ---
>
> Prof. Dr. Marcos Verissimo Alves
> Prof. Adjunto II, Curso de Física Computacional
> Instituto de Ciências Exatas
> Universidade Federal Fluminense
> Volta Redonda - RJ, Brasil
>
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