VMD-L Mailing List

From: Aravinda Munasinghe (aravinda1879_at_gmail.com)
Date: Sun Nov 29 2020 - 09:20:28 CST

Also, I see that you are trying to read in the psf file, therefore the
"topology" is taken from the "psf file" and not from the
"model.000.01_autopsf-temp.top". That's why you are getting the "psfgen)
duplicate topology file model.000.01_autopsf-temp.top" warning. And because
of that, you will not be able to add missing hydrogens from the "topology"
file (I am not sure why you are not used a default charmm topology file to
build the molecule in the first place, also assuming you want to use CHARMM
FF). :)
Best,
Aravinda

Aravinda Munasinghe

On Sun, Nov 29, 2020 at 10:11 AM Aravinda Munasinghe <aravinda1879_at_gmail.com>
wrote:

> 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
>>>>
>>>