From: Sanjay Hari (shari_at_universalsequencing.com)
Date: Mon Oct 05 2020 - 10:31:16 CDT
>From the archives, 2006:
--- JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:
> Since it's only the last two atoms of your protein,
> you could get away with
> letting psfgen guess their coordinates.
> Alternatively, you could manually
> edit your pdb file to change the names of just those
> two atoms (from O to
> OT1 and OXT to OT2) and then run psfgen.
________________________________
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of divyabharathi korlepara <divyabharathik938_at_gmail.com>
Sent: Monday, October 5, 2020 11:13:35 AM
To: namd-l_at_ks.uiuc.edu <namd-l_at_ks.uiuc.edu>
Subject: namd-l: psf generation
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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