psf generation

From: divyabharathi korlepara (divyabharathik938_at_gmail.com)
Date: Mon Oct 05 2020 - 10:13:35 CDT

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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