VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sun Nov 29 2020 - 10:15:42 CST

Also when I initially did use the Automatic PSF Builder in VMD, I used the
default charmm topology files.

On Sun, Nov 29, 2020 at 10:38 AM Isuru Herath <ish9_at_cornell.edu> wrote:

> Thank you for all the information. I am still not quite clear on how one
> molecule should only have unique resids. I used the Automatic PSF Builder
> in VMD, and that was the result. I ended up using the CHARMM-GUI PDB Reader
> to generate the psf and pdb files for this protein, and the script ran
> without errors. Is that correct? That also had multiple lines for each
> resid. Thanks again for your help.
>
> On Sun, Nov 29, 2020 at 10:30 AM Aravinda Munasinghe <
> aravinda1879_at_gmail.com> wrote:
>
>> So make sure you dont have resid 26 and segname AP1 in the other
>> structure you are trying to load. To merge structures you can also use the
>> MergeStructs Plugin it can handle most conflicts.
>> https://www.ks.uiuc.edu/Research/vmd/plugins/mergestructs/
>>
>> Aravinda Munasinghe
>>
>>
>> On Sun, Nov 29, 2020 at 10:24 AM Isuru Herath <ish9_at_cornell.edu> wrote:
>>
>>> 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
>>>>>>
>>>>>