VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Thu Oct 26 2023 - 13:53:06 CDT

Hi Bill,

LINK is the patch for a donut peptide, which is what you want. Its in
the default top_all36m_prot.rtf that the MacKerell group distributes
https://urldefense.com/v3/__http://mackerell.umaryland.edu/charmm_ff.shtml__;!!DZ3fjg!61SxavizS1nUy4x1YLxiTfN9W-Rtr8FLH8PcHtsL7phBpXJZ5PP9hq2iQqigqD72ZZWeFLWbcRcE4XyapZ0$

-Josh

On 10/26/23 1:34 PM, Bill McIntyre wrote:
> 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!61SxavizS1nUy4x1YLxiTfN9W-Rtr8FLH8PcHtsL7phBpXJZ5PP9hq2iQqigqD72ZZWeFLWbcRcEGnA9uig$
> <https://urldefense.com/v3/__https://esmatlas.com/resources?action=fold__;!!HXCxUKc!yZsZv5cJqaK_GuUPBu8rit2jKuaFDf3KfhOZzCi98X6g-no4YMz6UVVhXqjXkJtPI1a8bVW6FkbeqaRLjn8ySPiJ_9Gg$>
> 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/
>> <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>
>> <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.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 <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 

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