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From: Bill McIntyre (bill_mcintyre378_at_outlook.com)
Date: Thu Oct 26 2023 - 12:34:12 CDT
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Hi Josh,
Thanks for bringing up the structure prediction approach, I checked out the website and it does look much more straightforward.
Now, since I want to make a simple N-terminus to C-terminus connection for my cyclic peptides (i.e. no braided torus structure), which patch should I use, LINK or LIG1?
Also, from where do I get/obtain the needed patch?
Thanks!
Bill
________________________________
From: Josh <vermaasj_at_msu.edu>
Sent: Wednesday, October 25, 2023 9:01 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,
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!5OKhvFWjoai85jDm7sfHIYbjpN3zr4hJWDRfKIb2yJQ4HtST1JVCIUS5cIw8W7KUzdHz7OVz-yU7q_JY_KYt8CiPUznrjw$ 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><mailto:vermaasj_at_msu.edu>
Sent: Tuesday, October 24, 2023 8:29 AM
To: Bill McIntyre <bill_mcintyre378_at_outlook.com><mailto:bill_mcintyre378_at_outlook.com>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto: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/ -Josh
From: Bill McIntyre <bill_mcintyre378_at_outlook.com><mailto:bill_mcintyre378_at_outlook.com>
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><mailto:vermaasj_at_msu.edu>
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 Bill McIntyre
Date: Tuesday, October 24, 2023 at 1:52 AM
To: "Vermaas, Josh" <vermaasj_at_msu.edu><mailto:vermaasj_at_msu.edu>, "vmd-l_at_ks.uiuc.edu"<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Script to Build Cyclic Peptides
Sent: Monday, October 23, 2023 7:57 AM
To: Bill McIntyre <bill_mcintyre378_at_outlook.com><mailto:bill_mcintyre378_at_outlook.com>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Script to Build Cyclic Peptides
--
Josh Vermaas
vermaasj_at_msu.edu<mailto: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<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io