VMD-L Mailing List

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Sun Nov 29 2020 - 09:11:45 CST

When you use psfgen within VMD, a molecule can only have "unique resids".
You can have the same resid within a "molecule" but with different
segnames. Can you share the complete tcl script/commands you used till this
point along with psf and pdb files? it would be easy to find the cause in
that way.
Also to answer your question, PSFGEN cannot handle duplicates with atom
names in the same residue as well as structures with the same resid within
a single segment.
Best,
Aravinda Munasinge

'Aravinda Munasinghe

On Sun, Nov 29, 2020 at 10:03 AM Isuru Herath <ish9_at_cornell.edu> wrote:

> Thank you for the suggestion. Within the AP1 segment the only rows with
> the resid 26 were the 14 rows I showed. Correct me if I am wrong (I am new
> to NAMD), but aren't those referring to the same residue just different
> atoms?
>
> Thanks,
> Isuru
>
> On Sun, Nov 29, 2020 at 9:49 AM Aravinda Munasinghe <
> aravinda1879_at_gmail.com> wrote:
>
>> 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
>>>
>>