VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Wed Oct 25 2023 - 09:01:37 CDT

Hi Bill,

Yeah, something like that should be possible, depending on your text
file format. I'm used to operating under the assumption that you have a
pdb structure, either from experimental determination or structure
prediction methods. If you have a set of sequences already in mind, I
think passing those sequences to AlphaFold or ESMFold will probably be
your fastest way forward. https://urldefense.com/v3/__https://esmatlas.com/resources?action=fold__;!!DZ3fjg!_joQVFboq0vqz7xJmQfXZTBnvdqr3k7VejLnZOPOmW2BqBtHtUXG62IxNN3D6oM3iu-z7B6Dimc4qOi3sdo$ has
returned basically instantly for every sequence I've thrown at it so far.

The reason I think structure prediction methods are the way forward for
you is that the "let psfgen guess the coordinates" method for the
backbone will make a perfectly linear structure, with one REALLY long
bond connecting the ends. So while its technically possible to make a
linear polypeptide by just specifying all the residues one at a time:

segment C {

residue 1 MET

residue 2 ALA

..

residue 100 GLU

first none

last none

}

This will be more work I think.

-Josh

On 10/25/23 7:20 AM, Bill McIntyre wrote:
> Hi Josh,
>
> Thanks for the script.  So it sounds like in order to make a cyclic
> peptide I must have a pre-existing linear pdb file version of the
> peptide already made.
>
> If this is the case, is it possible then to make the linear version of
> the peptide first by using tkl/tkCon scripting by supplying the tkl
> script a simple text file listing my sequences and have each sequence
> made programmatically and the resulting pdb files saved to a folder?
>
> I'm thinking I can probably have my workflow first read the text file
> to make a linear peptide then have your provided script make the
> cyclic version.  Thanks for all your help.
>
> Bill
> ------------------------------------------------------------------------
> *From:* Vermaas, Josh <vermaasj_at_msu.edu>
> *Sent:* Tuesday, October 24, 2023 8:29 AM
> *To:* Bill McIntyre <bill_mcintyre378_at_outlook.com>; vmd-l_at_ks.uiuc.edu
> <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: Script to Build Cyclic Peptides
>
> Hi Bill,
>
> The basic script is basically what the previous poster showed.
> Assuming a pdb with the sequence already there (it just isn’t
> connected), called file.pdb with segname C, I’d do something like this:
>
> package require psfgen
>
> topology top_all36_prot.rtf
>
> segment C {
>
> pdb file.pdb
>
> first none
>
> last none
>
> }
>
> #I need to know the last residue number
>
> mol new file.pdb
>
> set sel [atomselect top “name CA”]
>
> set lastresid [lindex [$sel get resid] end]
>
> #Apply the patch
>
> patch LINK C:[expr {$lastresid – 1}] C:$lastresid C:1 C:2
>
> #Add coordinates and do the rest of the psf building.
>
> coordpdb file.pdb C
>
> regenerate angles dihedrals
>
> guesscoord
>
> writepsf out.psf
>
> writepdb out.pdb
>
> The coordinates are going to look all kinds of goofy, since psfgen
> won’t change them, and you may need to run some short minimization or
> equilibration simulations so that the long bond connecting the two
> ends of the protein doesn’t look ridiculous. You’ll probably also need
> to check if you get the appropriate chirality you expect between the
> N- and C- terminal linkage after minimization. I **think** the
> Chirality plugin can handle this,
> https://www.ks.uiuc.edu/Research/vmd/plugins/chirality/
> <https://urldefense.com/v3/__https://www.ks.uiuc.edu/Research/vmd/plugins/chirality/__;!!HXCxUKc!3f4GFtEAYOOWz2PgDzxxeDdZL5I_7aJvJN-o8r0OI2MuUdYjXPUa6JyJpiLY-YZiv8oU5vK_7ksZTTvEwGg8_44J60Up$>
> but I’m not positive.
>
> -Josh
>
> *From: *Bill McIntyre <bill_mcintyre378_at_outlook.com>
> *Date: *Tuesday, October 24, 2023 at 1:52 AM
> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>, "vmd-l_at_ks.uiuc.edu"
> <vmd-l_at_ks.uiuc.edu>
> *Subject: *Re: vmd-l: Script to Build Cyclic Peptides
>
> Hi Josh,
>
> Thank you for clarifying that.  Now the situation is that besides
> using the GUI for Molefacture to build a simple linear peptide, I have
> never built cyclic peptides (N to C connection) using VMD nor have I
> ever scripted building a peptide in VMD either.
>
> Would you please advise me or direct me to where/who I can go to for
> building my cyclic (N to C connection) peptides? I have many of these
> to build so would you please point me to how I can build such cyclic
> peptides with a TKL script perhaps?  I do not need to make psf files
> for them, just a series of simple pdb files for each sequence.  Thanks.
>
> Bill
>
> ------------------------------------------------------------------------
>
> *From:*Josh <vermaasj_at_msu.edu>
> *Sent:* Monday, October 23, 2023 7:57 AM
> *To:* Bill McIntyre <bill_mcintyre378_at_outlook.com>; vmd-l_at_ks.uiuc.edu
> <vmd-l_at_ks.uiuc.edu>
> *Subject:* Re: vmd-l: Script to Build Cyclic Peptides
>
> Hi Bill,
>
> That previous post has most of it. The initial poster just couldn't
> have the automatic first and last patches applied and still have it
> work. Basically, a cyclic peptide is like any other, but at some point
> you end up forcing a coupling that isn't what you'd expect for a
> linear polymer. In CHARMM36, this weird topology can be described by
> the LINK patch if you want to make a torus, or LIG1 if the loop is
> internal somewhere.
>
> -Josh
>
> On 10/22/23 6:38 PM, Bill McIntyre wrote:
>
> Hello everyone,
>
> Would someone please kindly provide me with some direction on how
> to make a script to build cyclic peptides in VMD from a provided
> list of sequences?  An output of PDB files for the sequences is
> sufficient (one separate PDB file per sequence).
>
> I saw there was a discussion in a previous mail posting that
> touched on this subject
> (https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0961.html
> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2015-2016/0961.html__;!!HXCxUKc!21eBJ0NmTHVDf9x5FGwAWMQMsEXUNaYkk4A8z0VNGMsjc7iJZneLUbcDfyVNlxVMkQpd0xPOCp97QICEK0SHqB1WIoWC$>)
> but I didn't see any follow up that could guide me in doing this
> task.  Thanks.
>
> Bill McIntyre
>
>
>
> --
> Josh Vermaas
>
> vermaasj_at_msu.edu
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
> Michigan State University
> vermaaslab.github.io 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io