VMD-L Mailing List

From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Fri Jul 24 2015 - 07:12:09 CDT

Hi,

Neither the topology nor the psfgen packages need to be loaded more than
once, so they should be outside the loop. Also, at the end of the loop
you should do resetpsf the clean the topology in the memory.

Felipe

On 24/07/15 08:25, Matthew Stewart wrote:
>
> 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
>
> CRICOS Provider No. 00124K (Melbourne)
> CRICOS Provider No. 02475D (Sydney)
>
> http://intranet.vu.edu.au/mcd/Logo-intranet.jpg <http://www.vu.edu.au/>
>
> This email and any files transmitted with it are confidential and are
> intended solely for the use of the individual or entity to whom they
> are addressed. If you have received this email in error please notify
> the system manager. Please note that any views or opinions presented
> in this email are solely those of the author and do not necessarily
> represent those of Victoria University.
>
> *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
>
> This email, including any attachment, is intended solely for the use
> of the intended recipient. It is confidential and may contain personal
> information or be subject to legal professional privilege. If you are
> not the intended recipient any use, disclosure, reproduction or
> storage of it is unauthorised. If you have received this email in
> error, please advise the sender via return email and delete it from
> your system immediately. Victoria University does not warrant that
> this email is free from viruses or defects and accepts no liability
> for any damage caused by such viruses or defects.
>