VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sun Nov 29 2020 - 10:22:56 CST

Oh okay, that makes sense now. Thank you very much! Using the MergeStruct
plugin automatically prompted me to change the segids.

Thank you,
Isuru Herath

On Sun, Nov 29, 2020 at 11:20 AM Aravinda Munasinghe <aravinda1879_at_gmail.com>
wrote:

> It is not that you must have unique segIDs in a molecule, but must have
> unique segids in one segment. You can have multiple segments in one
> molecule (Ie. each chain with a different segname). What you can do is to
> use simple VMD commands to rename the segnames.
>
> i.e. set aa [atomselect top "segname AP1"]
> $aa set segname T1
>
> and write the new PSF and PDB and use them to join structures,
>
> You can use CHARMM-GUI to make PSF and PDB files, it also automatically
> adds missing atoms (including Hs). Just make sure to use segnames that are
> not common when you are using your script.
> Best,
> AM
>
> Aravinda Munasinghe
>
>
> 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
>>>>>>>
>>>>>>