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From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Tue Jul 28 2015 - 01:16:02 CDT

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<mailto: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<mailto: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<mailto: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--_000_B7E2246B115A4C7AAA7BF868BEC9D166quteduau_--