VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sat Nov 28 2020 - 13:01:55 CST

Hello,

I was trying to run the command "readpsf model.000.01.Alig_autopsf.psf."
This resulted in the following error:

"psfgen) reading structure from psf file model.000.01.Alig_autopsf.psf
psfgen) duplicate topology file model.000.01_autopsf-temp.top
psfgen) Unable to add (duplicate?) residue AP1:26

MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over."

I would really appreciate any suggestions on how to fix this.

The beginning of the model.000.01.Alig_autopsf.psf file looks like this:

"
PSF

       9 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 4 patches were applied to the molecule.
 REMARKS topology model.000.01_autopsf-temp.top
 REMARKS segment AP1 { first NTER; last CTER; auto angles dihedrals }
 REMARKS segment AP2 { first NTER; last CTER; auto angles dihedrals }
 REMARKS patch CTER AP1:68
 REMARKS patch NTER AP1:26
 REMARKS patch CTER AP2:108
 REMARKS patch NTER AP2:73

     765 !NATOM
       1 AP1 26 PHE HT1 HC 0.350000 1.0080 0
       2 AP1 26 PHE HT2 HC 0.350000 1.0080 0
       3 AP1 26 PHE N NH3 -0.300000 14.0070 0
       4 AP1 26 PHE HT3 HC 0.350000 1.0080 0
       5 AP1 26 PHE CA CH1E 0.250000 13.0190 0
       6 AP1 26 PHE CB CH2E 0.000000 14.0270 0
       7 AP1 26 PHE CG C 0.000000 12.0110 0
       8 AP1 26 PHE CD1 CR1E 0.000000 13.0190 0
       9 AP1 26 PHE CD2 CR1E 0.000000 13.0190 0
      10 AP1 26 PHE CE1 CR1E 0.000000 13.0190 0
      11 AP1 26 PHE CE2 CR1E 0.000000 13.0190 0
      12 AP1 26 PHE CZ CR1E 0.000000 13.0190 0
      13 AP1 26 PHE C C 0.550000 12.0110 0
      14 AP1 26 PHE O O -0.550000 15.9990 0
      15 AP1 27 ASP N NH1 -0.350000 14.0070 0
      16 AP1 27 ASP H H 0.250000 1.0080 0
      17 AP1 27 ASP CA CH1E 0.100000 13.0190 0
      18 AP1 27 ASP CB CH2E -0.160000 14.0270 0"

Any help would be greatly appreciated.

Thank you,
Isuru