VMD-L Mailing List

From: Isuru Herath (ish9_at_cornell.edu)
Date: Sun Nov 29 2020 - 09:03:17 CST

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
>>
>