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From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri Oct 27 2023 - 17:15:02 CDT

Next message: Bill McIntyre: "Re: Script to Build Cyclic Peptides"
Previous message: Smith, Harper E.: "Re: Creating Dummy Atoms in VMD Using TCL Script"
In reply to: Patrick Charchar: "Re: Script to Build Cyclic Peptides"
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Hi Patrick,

Psfgen needs at least a few coordinates to get started when it starts guessing. What psfgen is doing is following the “rules” encoded in the topology file, using the IC table to build new coordinates from existing coordinates. You’ll need 3 atoms at minimum for psfgen to be able to guess the rest of the positions, and when I’ve done this in the past, I’ve used the N, C, and CA atoms from a random pdb structure to seed a first residue.

-Josh

From: Patrick Charchar <patrick.charchar_at_rmit.edu.au>
Date: Thursday, October 26, 2023 at 8:02 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>, 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

RMIT Classification: Trusted

Hi again,

As an update this is where I got:

psfcontext reset
topology {top_all36_prot.rtf}
segment C {residue 1 MET}
guesscoord
regenerate angles dihedrals
writepsf "out.psf"
writepdb "out.pdb"

psfcontext reset
topology {top_all36_prot.rtf}
segment C { pdb "out.pdb" ; first NTER; last CTER; auto angles dihedrals }
coordpdb "out.pdb" C
guesscoord
writepsf "out2.psf"
writepdb "out2.pdb"

The psf looks great and the pdb contains all relevant atoms, names etc but the coordinates are all zero. Not sure I’m using guesscoord correctly… any tips would be greatly appreciated. Once I have the syntax down would be keen get this approach working with psfgen to generate both linear and then cyclic polypeptides (with LINK patch).

Thanks again,
Patrick

psfgen) clearing structure, topology, and aliases
psfgen) reading topology file top_all36_prot.rtf

psfgen) >>>>>>>>CHARMM36 All-Hydrogen Topology File for Proteins <<<<<<
psfgen) >>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<
psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> May 2011 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
psfgen) All comments to the CHARMM web site: https://urldefense.com/v3/__http://www.charmm.org__;!!DZ3fjg!6oTXG_9fi6P0IZ_epFBKVff6PNtvrfZ2MaxEUN9bv4Xtd9lMEuc_FXajwwLhwht32u9S2XKLBJDE21K6IIg$
psfgen) parameter set discussion forum
psfgen)
psfgen) Created by CHARMM version 36 1
psfgen) ERROR! Failed to parse autogenerate statement. Line 95: AUTO ANGLES DIHE PATCH

psfgen) cross-term entries present in topology definitions
psfgen) building segment C
psfgen) Info: generating structure...psfgen) Info: skipping bond C-N at beginning of segment.
psfgen) Info: skipping improper C-CA-N-O at beginning of segment.
psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation CA-C-N-CA at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-O at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
segment complete.
psfgen) Info: guessing coordinates for 20 atoms (9 non-hydrogen)
psfgen) Warning: failed to guess coordinates for 20 atoms
psfgen) regenerating all angles
psfgen) regenerating all dihedrals
psfgen) Info: writing psf file out.psf
psfgen) total of 20 atoms
psfgen) total of 19 bonds
psfgen) total of 34 angles
psfgen) total of 39 dihedrals
psfgen) total of 1 impropers
psfgen) total of 0 explicit exclusions
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file out.pdb
psfgen) Info: pdb file complete.
psfgen) clearing structure, topology, and aliases
psfgen) reading topology file top_all36_prot.rtf

psfgen) cross-term entries present in topology definitions
psfgen) building segment C
psfgen) reading residues from pdb file out.pdb
psfgen) extracted 1 residues from pdb file
psfgen) setting patch for first residue to NTER
psfgen) setting patch for last residue to CTER
psfgen) enabling angle autogeneration
psfgen) enabling dihedral autogeneration
psfgen) Info: generating structure...psfgen) Info: skipping bond C-N at beginning of segment.
psfgen) Info: skipping improper C-CA-N-O at beginning of segment.
psfgen) Info: skipping improper N-C-CA-HN at beginning of segment.
psfgen) Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation CA-C-N-CA at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-O at beginning of segment.
psfgen) Info: skipping conformation N-CA-C-N at beginning of segment.
psfgen) Info: skipping conformation C-N-CA-C at beginning of segment.
psfgen) Info: skipping conformation C-CA-N-HN at beginning of segment.
segment complete.
psfgen) reading coordinates from pdb file out.pdb for segment C
psfgen) Info: guessing coordinates for 0 atoms (0 non-hydrogen)
psfgen) Info: writing psf file out2.psf
psfgen) total of 20 atoms
psfgen) total of 19 bonds
psfgen) total of 34 angles
psfgen) total of 39 dihedrals
psfgen) total of 1 impropers
psfgen) total of 0 explicit exclusions
psfgen) total of 0 cross-terms
psfgen) Info: psf file complete.
psfgen) Info: writing pdb file out2.pdb
psfgen) Info: pdb file complete.

From: Patrick Charchar <patrick.charchar_at_rmit.edu.au>
Date: Friday, 27 October 2023 at 9:31 am
To: Josh <vermaasj_at_msu.edu>, 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 Josh, Bill, and all,

I’m just curious on this comment to generate a linear (not cyclic) pdb from a primary sequence using psfgen.

Can you please direct me to what I’m missing here?

mol new atoms 20
psfcontext reset
topology {top_all36_prot.rtf}
segment C {residue 1 MET}
guesscoord
psfgen) clearing structure, topology, and aliases
psfgen) reading topology file /Users/patricknotpeter/Desktop/top_all36_prot.rtf

Thanks,
Patrick

From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Josh <vermaasj_at_msu.edu>
Date: Thursday, 26 October 2023 at 7:23 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!6oTXG_9fi6P0IZ_epFBKVff6PNtvrfZ2MaxEUN9bv4Xtd9lMEuc_FXajwwLhwht32u9S2XKLBJDEU0G9fpA$ <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><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/$> but I’m not positive.

-Josh

From: Bill McIntyre <bill_mcintyre378_at_outlook.com><mailto:bill_mcintyre378_at_outlook.com>
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

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>
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

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.html0xPOCp97QICEK0SHqB1WIoWC$>) 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<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

Next message: Bill McIntyre: "Re: Script to Build Cyclic Peptides"
Previous message: Smith, Harper E.: "Re: Creating Dummy Atoms in VMD Using TCL Script"
In reply to: Patrick Charchar: "Re: Script to Build Cyclic Peptides"
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