VMD-L Mailing List

From: Matthew Stewart (Matthew.Stewart_at_vu.edu.au)
Date: Fri Jul 24 2015 - 01:25:58 CDT

Hi Akshay,

You need to read in the segments and coordinates – I have added the code below in red. I would also recommend another change as well, as this will write files that are .pdb.pdb or .pdb.psf as the $file includes the file extension. The change in blue will fix this.

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

This should work – let me know if it doesn’t…

Regards,
Matt Stewart

Dr. Matthew B. Stewart
Postdoctoral Research Fellow
Institute for Sustainability and Innovation
Werribee Campus, Victoria University
Phone: +61 3 9919 7641
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From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Akshay Bhatnagar
Sent: Friday, 24 July 2015 2:34 PM
To: Josh Vermaas
Cc: Ashar Malik; vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Generating PSF for several proteins in one shot

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<mailto: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<mailto: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




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