VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sun Nov 29 2020 - 08:58:31 CST

Correction: instead of step1_pdbreader.psf I used the
model.000.01.Alig_autopsf.psf
file.

On Sun, Nov 29, 2020 at 9:56 AM Isuru Herath <ish9_at_cornell.edu> wrote:

> Thank you for your response, I was trying to combine two PSF files for two
> proteins into one. One of them ran without errors, but with this one I got
> an error. The script for combining them looked like this:
>
> "package require psfgen
>
> resetpsf
>
>
>
>
> readpsf protein_autopsf.psf
>
> readpsf step1_pdbreader.psf
>
>
> coordpdb protein_autopsf.pdb
>
> coordpdb step1_pdbreader.pdb
>
>
> writepsf all.psf
>
> writepdb all.pdb
>
>
> puts "HE TERMINADO!!!!"
>
>
> quit"
>
> On Sat, Nov 28, 2020 at 7:03 PM Peter Freddolino <petefred_at_umich.edu>
> wrote:
>
>> Could you please let us know in what context you're using the readpsf
>> command? What are you trying to do? In most usage cases (eg, if you're
>> trying to load a molecule for visualization), what you're actually looking
>> for is
>> mol new model.000.01.Alig_autopsf.psf
>>
>> Best,
>> Peter
>>
>> On Sat, Nov 28, 2020 at 3:42 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
>>>
>>