VMD-L Mailing List

From: Marcos Verissimo Alves (marcos_verissimo_at_id.uff.br)
Date: Mon Apr 06 2020 - 12:04:07 CDT

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, the same that has been reported on March 09 by
user Jing Liang. Here I provide a bit more info on the steps I took to
attempt to generate input files with QwikMD - I apologize if the e-mail is
a bit too long.

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 "FAV" (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 FAV 0.00
(...)

2 - Pre-processed the protein file with QwikMD (generated input files with
no problems).

3 - Took the protein coordinates from step 2, 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 4643 C THR A 304 -5.415 -10.209 -16.484 0.00 0.00 AP1
 C
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
ATOM 1 C1 FAV A 305 4.473 -27.094 21.158 0.00 0.00 FAV
 C
ATOM 2 C2 FAV A 305 4.276 -28.495 21.183 0.00 0.00 FAV
 C
ATOM 3 N1 FAV A 305 3.071 -29.050 21.037 0.00 0.00 FAV
 N
ATOM 4 C3 FAV A 305 2.028 -28.242 20.860 0.00 0.00 FAV
 C
ATOM 5 C4 FAV A 305 2.231 -26.862 20.837 0.00 0.00 FAV
 C
ATOM 6 N2 FAV A 305 3.405 -26.302 20.979 0.00 0.00 FAV
 N
ATOM 7 H FAV A 305 6.882 -28.125 21.472 0.00 0.00 FAV
ATOM 8 N FAV A 305 6.904 -27.114 21.456 0.00 0.00 FAV
 N
ATOM 9 H1 FAV A 305 7.786 -26.633 21.569 0.00 0.00 FAV
ATOM 10 C FAV A 305 5.793 -26.356 21.318 0.00 0.00 FAV
 C
ATOM 11 O FAV A 305 5.820 -25.124 21.315 0.00 0.00 FAV
 O
ATOM 12 O1 FAV A 305 5.318 -29.333 21.362 0.00 0.00 FAV
 O
ATOM 13 H2 FAV A 305 4.979 -30.248 21.337 0.00 0.00 FAV
ATOM 14 H3 FAV A 305 1.041 -28.680 20.740 0.00 0.00 FAV
ATOM 15 F FAV A 305 1.182 -26.047 20.660 0.00 0.00 FAV
 F

3 - Copied the Swissparam fav.rtf
to /usr/local/lib/vmd/plugins/noarch/tcl/readcharmmtop1.2/ and loaded
"complex.pdb" to QwikMD; the complex was displayed correctly in the OpenGL
display and no warnings were issued (no requests to open "Structure
manipulation"). 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:

(...)
AP1:304
AP1:1
segment complete.
psfgen) reading coordinates from pdb file
prot_lig_formatted_autopsf-temp.pdb_AP1.pdb for segment AP1
segfiles prot_lig_formatted_autopsf-temp.pdb_AP1.pdb
prot_lig_formatted_autopsf-temp.pdb_AO1.pdb
prot_lig_formatted_autopsf-temp.pdb_AO1.pdb
4646 4659
psfgen) building segment AO1
psfgen) reading residues from pdb file
prot_lig_formatted_autopsf-temp.pdb_AO1.pdb
psfgen) unknown residue type FAV
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 FAV
failed!

Am I doing something wrong or missing anything?

Best regards,

Marcos 

---
Dr. Marcos Verissimo Alves
Prof. Adjunto II, Curso de Física Computacional
Instituto de Ciências Exatas
Universidade Federal Fluminense
Volta Redonda - RJ, Brasil