Re: psf generation

From: Pratik Narain Srivastava (pratik.narain_at_gmail.com)
Date: Tue Oct 06 2020 - 01:37:04 CDT

Try autopsf as suggested above and do look at its log. It has some valuable
information.

On Tue, Oct 6, 2020, 11:18 AM divyabharathi korlepara <
divyabharathik938_at_gmail.com> wrote:

> 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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