VMD-L Mailing List

From: Daniel Möller (daniel.moeller3_at_uni-greifswald.de)
Date: Sat Aug 08 2015 - 05:39:58 CDT

Hi,

it’s in your script:

 

pdbalias residue HIS HSE

 

 

Sincerely

 

Daniel Möller

 

 

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Akshay Bhatnagar
Gesendet: Samstag, 8. August 2015 10:36
An: Tristan Croll
Cc: Josh Vermaas; Ashar Malik; vmd-l_at_ks.uiuc.edu
Betreff: Re: vmd-l: Generating PSF for several proteins in one shot

 

Hello

I have got the script working. It is like this:

set filelist [glob *.PDB]
  foreach file $filelist {
    mol new $file
    set name [file rootname $file]
    set selp [atomselect top protein]
    echo $selp
    $selp writepdb $file-1.pdb
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
pdbalias atom LYS 1HZ HZ1
pdbalias atom LYS 2HZ HZ2
pdbalias atom LYS 3HZ HZ3
pdbalias atom ARG 1HH1 HH11
pdbalias atom ARG 2HH1 HH12
pdbalias atom ARG 1HH2 HH21
pdbalias atom ARG 2HH2 HH22
pdbalias atom ASN 1HD2 HD21
pdbalias atom ASN 2HD2 HD22
pdbalias atom SER HG HG1
segment U {pdb $file-1.pdb}
coordpdb $file-1.pdb U
guesscoord
writepdb $name-psf.pdb
writepsf $name-psf.psf
resetpsf
}

The only problem is i am getting an error :

psfgen) Info: generating structure...psfgen) unknown residue type HSE
failed!
ERROR: failed on end of segment
MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.

But i have thoroughly checked the pdb file, but there is no residue by the name 'HSE'. therefore i am unable to identify the actual problem. can any help please!!!

 

 

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Tue, Jul 28, 2015 at 11:46 AM, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:

Hi Akshay,

 

While you have "package require autopsf" in your script, you're not actually using AutoPSF. All the commands in your script are still psfgen ones. I'd suggest having a good read of the manual page for AutoPSF.

 

Cheers,

 

Tristan

 

 

Tristan Croll

Lecturer

Faculty of Health

School of Biomedical Sciences

Institute of Health and Biomedical Engineering

Queensland University of Technology

60 Musk Ave

Kelvin Grove QLD 4059 Australia

+61 7 3138 6443

 

This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

 

 

On 28 Jul 2015, at 4:10 pm, Akshay Bhatnagar <akshaybhatnagar2790_at_gmail.com> wrote:

As suggested i have changed the script accordingly. But the errors are same, i.e it is considering every residue as duplicate residue and giving an error in psf generation.

The script is:

package require autopsf
topology top_all27_prot_lipid.inp
set filelist [glob *.PDB]
  foreach file $filelist {
set name [file rootname $file]
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CDsource
segment A {pdb $file}
coordpdb $file A
writepdb $name.pdb
writepsf $name.psf
resetpsf
}
  

Please help. i am not able to find the defect in the script.

 

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Sat, Jul 25, 2015 at 4:30 AM, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:

You would be much better off using AutoPSF for a task like this. PSFgen alone will treat your protein like a single connected chain (so residues either side of a gap will become connected to each other) and, as you have already discovered, won't automatically handle ligands. AutoPSF is the front-end that handles all of that before feeding to PSFgen, and can be called from a non-interactive script.

 

Cheers,

 

Tristan

 

 

Tristan Croll

Lecturer

Faculty of Health

School of Biomedical Sciences

Institute of Health and Biomedical Engineering

Queensland University of Technology

60 Musk Ave

Kelvin Grove QLD 4059 Australia

+61 7 3138 6443

 

This email and its attachments (if any) contain confidential information intended for use by the addressee and may be privileged. We do not waive any confidentiality, privilege or copyright associated with the email or the attachments. If you are not the intended addressee, you must not use, transmit, disclose or copy the email or any attachments. If you receive this email by mistake, please notify the sender immediately and delete the original email.

 

 

On 24 Jul 2015, at 3:25 pm, Akshay Bhatnagar <akshaybhatnagar2790_at_gmail.com> wrote:

Thank you very much for your suggestions.

As you said, i have started with the tcl script (shown below), i am able to upload all the molecules in one go, but for some reason the output psf and pdb do not show any atoms. can anyone please help me to correct the script.

the script is:

set filelist [glob *.PDB]
  foreach file $filelist {
    mol new $file
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
writepdb $file.pdb
writepsf $file.psf
}

Your help is greatly appreciated.

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus

 

 

On Wed, Jul 22, 2015 at 12:14 AM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

Just an FYI, this usually won't work particularly well unless the proteins are well behaved. Usually there are missing pieces in pdb files that need manual intervention. That being said, autopsf has a tcl interface:

package require autopsf
autopsf -mol top -top topologyfilehere

Check the other autopsf options to see if they might be useful to you.

-Josh Vermaas

 

On 07/21/2015 02:33 AM, Ashar Malik wrote:

To start you off, make a list of all the pdb. Read them into a tcl script. Run a for loop for the number of pdb files you have and in each loop use the psfgen package.

Try it. If you are still stuck .. Drop another email.

On Jul 21, 2015 12:19 PM, "Akshay Bhatnagar" <akshaybhatnagar2790_at_gmail.com> wrote:

Hello everyone

I have around 5000 proteins and i want to generate 5000 psf and subsequently generated pdb files for all these 5000 proteins in one shot. I have always use automatic psf generate method to generate psf. Now please anyone help in generating a tcl script through which i can generate all the 5000 psf and pdb files in one go using the script.

With Regards

Akshay Bhatnagar

PhD Student

BITS Pilani Hyderabad Campus