VMD-L Mailing List

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Sun Nov 29 2020 - 08:48:32 CST

Most probably you may have the same resid in a single segment. PSFGEN won't
allow you to have the same resid within a single segname. You may want to
change that. check if segname AP1 has another resid 26.
Best,
Aravinda

Aravinda Munasinghe

On Sat, Nov 28, 2020 at 2:28 PM Isuru Herath <ish9_at_cornell.edu> wrote:

> 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
>