From: Ashkan Shekaari (shekaari_at_email.kntu.ac.ir)
Date: Mon Oct 05 2020 - 13:52:43 CDT
Dear researcher,
USE VMD > Extensions > Modeling > Automatic PSF Builder
in case you are a first-timer.
--
All the best,
Ashkan Shekaari,
Ph.D Candidate in Solid State Physics,
K. N. Toosi University of Technology,
Tehran, Iran
From: "divyabharathi korlepara" <divyabharathik938_at_gmail.com>
To: "namd-l" <namd-l_at_ks.uiuc.edu>
Sent: Monday, October 5, 2020 6:43:35 PM
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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