From: divyabharathi korlepara (divyabharathik938_at_gmail.com)
Date: Tue Oct 06 2020 - 00:45:24 CDT
Hi,
I could create the psf files. while I am trying to open the psf files
with "readpsf" command it is giving me the error.
*MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.*
Thanks,
Divya.
Dr. Divya Bharathi,
Post Doctoral Fellow,
IIIT
Hyderabad-500032.
INDIA.
On Tue, Oct 6, 2020 at 12:22 AM Ashkan Shekaari <shekaari_at_email.kntu.ac.ir>
wrote:
> *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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