From: Marcos Verissimo Alves (marcos_verissimo_at_id.uff.br)
Date: Sun Apr 05 2020 - 00:33:57 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. 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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