VMD-L Mailing List

From: Akshay Bhatnagar (akshaybhatnagar2790_at_gmail.com)
Date: Fri Jul 24 2015 - 02:29:08 CDT

Thank you very much sir for the corrections, but it is still giving errors,
it it not able to remove the ligands because of which it is failing and is
ignoring all the amino acid residues and giving error as duplicate key.

With Regards
Akshay Bhatnagar
PhD Student
BITS Pilani Hyderabad Campus

On Fri, Jul 24, 2015 at 11:55 AM, Matthew Stewart <Matthew.Stewart_at_vu.edu.au
> 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)
>
> [image: 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>
> 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--089e0149416ea88ea8051b99f585--
--089e0149416ea88eb0051b99f586--