VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sun Nov 29 2020 - 08:56:47 CST

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
>>
>