From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Oct 05 2020 - 11:51:24 CDT
Hi Divya,
Guessing coordinates and regenerating angles and dihedrals are kind of my
goto.
The script would be:
package require psfgen
resetpsf
topology /home/divya/Downloads/toppar_c36_jul20/non_charmm/parm14sb_all.rtf
pdbalias residue HIS HIE
pdbalias residue HIS HID
pdbalias atom ILE CD1 CD
# Generating psf file for protein
segment P {pdb 4w52_protein_noh.pdb}
coordpdb 4w52_protein_noh.pdb P
regenerate angles dihedrals
guesscoord
writepsf output.psf
writepdb output.pdb
-Josh
On Mon, Oct 5, 2020 at 9:15 AM divyabharathi korlepara <
divyabharathik938_at_gmail.com> wrote:
> Dear NAMD users,
>
> I am new to namd and protein simulations. I am trying to
> simulate a protein-ligand system.
>
> The protein I am looking is 4w52, using amber force field i want to create
> psf file using the following script.
>
>
> package require psfgen
> resetpsf
>
> topology /home/divya/Downloads/toppar_c36_jul20/non_charmm/parm14sb_all.rtf
>
> pdbalias residue HIS HIE
> pdbalias residue HIS HID
> pdbalias atom ILE CD1 CD
>
> # Generating psf file for protein
> segment P {pdb 4w52_protein_noh.pdb}
>
> At segment I am getting error:
>
> Info: skipping conformation C-N-CA-C at beginning of segment.
> psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
> psfgen) Info: skipping bond C-N at end of segment.
> psfgen) Info: skipping improper CA-N-C-O at end of segment.
> psfgen) Info: skipping conformation CA-C-N-CA at end of segment.
> psfgen) Info: skipping conformation N-CA-C-O at end of segment.
> psfgen) Info: skipping conformation N-CA-C-N at end of segment.
>
> coordpdb 4w52_protein_noh.pdb P
> vmd > coordpdb 4w52_protein_noh.pdb P
> psfgen) reading coordinates from pdb file 4w52_protein_noh.pdb for segment
> P
> psfgen) Warning: failed to set coordinate for atom O HID:172 P
> psfgen) Warning: failed to set coordinate for atom OXT HID:172 P
> vmd >
>
> I do not know how to solve this.
>
> Can someone help me with this.
>
> Awaiting reply,
>
> Thanks,
> Divya.
>
>
>
>
>
>
>
>
> Dr. Divya Bharathi,
> Post Doctoral Fellow,
> IIIT
> Hyderabad-500032.
> INDIA.
>
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