VMD-L Mailing List

From: Kyle Billings (krb_at_udel.edu)
Date: Thu Mar 28 2024 - 15:15:23 CDT

Thanks for the explanation Josh. I updated the TLC script I was using to
patch the residues to now read
------------------------------------------------------------------------------------------------------------------------------
foreach i {0 1 2 3} {
        # make the segment
        segment PRO$i {
                pdb parts/fixed_${i}.pdb
        }
        patch EETY PRO$i:77 PRO$i:78
        patch GLUP PRO$i:71
        coordpdb parts/fixed_${i}.pdb PRO$i
        regenerate angles dihedrals
}
-------------------------------------------------------------------------------------------------------------------------
 Unfortunately, the atom positions for the Tyr 78 OE and HA atoms positions
still fail to be guessed. The solution I am thinking of right is to
manually add in the IC parameters, for the EETY PRES, to allow psfgen to
better guess the atoms position . Is this actually worth the effort, or is
there a better way to build the protein?

Kyle

On Wed, Mar 27, 2024 at 10:51 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:

> Hi Kyle,
>
>
>
> Since until you patch the residues, the atom names probably won’t match
> what they should. The thing that is unintuitive about psfgen is that you
> need to hold two things in your head: 1.) The literal topology and identity
> of the atoms, and 2) The coordinates. The topology (how the atoms are
> bonded) and identity (atomtypes, masses, charges) all end up in the psf,
> and as the name suggests, this is what psfgen actually cares the most
> about. It is good practice to make sure that the topology is correct before
> setting coordinates, since PDB generation (the coordinates) is done by
> psfgen sort of as an afterthought. What psfgen does to set coordinates is
> it reads in the input pdb, and takes coordinates from atoms that have the
> same name, resid, and segname in the input, and assigns them to the output
> structure psfgen has in its memory. So if you coordpdb **before**
> patching, psfgen will dutifully assign all the atoms it knows about from
> the input structure (normal protein backbone, most of the sidechain). But
> since it hasn’t been patched yet, psfgen doesn’t know about the extra
> ester-specific atoms, which are only added after patching. If you patch
> after the coordpdb, psfgen will make those atoms exist, but they won’t have
> coordinates assigned, so the default is the origin.
>
>
>
> -Josh
>
>
>
> *From: *Kyle Billings <krb_at_udel.edu>
> *Date: *Tuesday, March 26, 2024 at 4:18 PM
> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
> *Subject: *Re: vmd-l: Atoms poorly guessed after applying a patch in
> Psfgen
>
>
>
> Thanks Josh,
>
>
>
> I must have not copied those lines into the intal post, but i am curious
> why you patched the residues before getting the coordinates of the molecule?
>
>
>
> Thanks for the help ,
>
> Kyle
>
>
>
> On Mon, Mar 25, 2024 at 4:01 PM Josh Vermaas <vermaasj_at_msu.edu> wrote:
>
> Hi Kyle,
>
> Where is the patch being applied? I don't see it in the script snippets.
> Based on the topology file you sent, I'd expect a patch command to be
> issued before you try to guess the coordinates. Patches get applied after
> segments. So your innermost loop would look something like this:
>
> segment PRO$i {
> pdb parts/fixed_${i}.pdb
> }
> #Apply the patch.
> patch EETY PRO$i:77 PRO$I:78
> # coord pdb
> coordpdb parts/fixed_${i}.pdb PRO$i
>
> regenerate angles dihedrals
>
> -Josh
>
>
>
> On 3/25/24 1:28 PM, Kyle Billings wrote:
>
> Hello Users,
>
>
>
> I am working on creating a psf/pdb using Psfgen to model an ester
> between the Gly77-Tyr78 of KcsA (PDB:4MSW). I found parameters to modify
> the ester linkage published from Li. et. al (
> https://urldefense.com/v3/__https://doi.org/10.1073/pnas.1706983114__;!!DZ3fjg!9rJlDLxS9uVwWcP04eIFFwhvp4goMy8tUz3CQPhSifO7AS04kSkAj-6sRhAHVH1Oitu_zAyBS2_hjA$
> <https://urldefense.com/v3/__https:/doi.org/10.1073/pnas.1706983114__;!!DZ3fjg!7NANVEnRX4o-lm715IR1fjoNBdHcy2zDmDRJcMQkTp89tzO1zO6hT5uQmDGsXeAEciouaoaTomL06g$>)
> and the file should be attached to this post. When applying the patch, the
> positions ester oxygen and the alpha carbon hydrogen atom of Tyr78 fail to
> be set. I was wondering if there is a flaw in my methodology that I am not
> seeing? I am sorry for the length of this message in advance.
>
>
>
> The current method is to convert manually the TYF 78 to TYR 78, because
> 4MSW already has the ester in the structure. This is to comply atom naming
> from the patch for each monomer of 4MSW.
>
>
> -----------------------------------------------------------------------------------------------
> for {set i 0} { $i < 4 } { incr i } {
> puts $i
> # load the ##_*.pdb
> mol load pdb 4MSW/${i}_4msw.pdb2.pdb
> # # select the atoms that we need to make
> [atomselect top "resname TYF and name C1 " ] set name C
> [atomselect top "resname TYF and name O1" ] set name O
> [atomselect top "resname TYF and name N" ] set type NH1
> [atomselect top "resname TYF and name C2" ] set name CA
> [atomselect top "resname TYF and name C3 " ] set name CB
> [atomselect top "resname TYF and name C4 " ] set name CG
> [atomselect top "resname TYF and name C5 " ] set name CD1
> [atomselect top "resname TYF and name C6 " ] set name CE1
> [atomselect top "resname TYF and name C7 " ] set name CZ
> [atomselect top "resname TYF and name C8 " ] set name CE2
> [atomselect top "resname TYF and name C9 " ] set name CD2
> [atomselect top "resname TYF and name O3"] set name OH
> [atomselect top "resname TYF "] set resname TYR
> [atomselect top "not (resname HOH TIP3 OH2 SOL DGA K)" ] writepdb
> parts/TEMP_fixed_${i}.pdb
> }
>
>
> -----------------------------------------------------------------------------------------------
>
>
>
> From there we can the newly made monomer pdb's to build the psf. I apply
> the pdbalias as stated in the Membrane Proteins Tutorial (Advanced), and
> load in the CHARMM36 topologies. After the adding the additional topology
> for the amide to ester mutation I build the psf/pdb a follows.
>
>
> -----------------------------------------------------------------------------------------------
>
> topology toppar/toppar_all36_amide_to_ester.str
>
>
>
> foreach i {0 1 2 3} {
> # make the segment
> segment PRO$i {
> pdb parts/fixed_${i}.pdb
> }
> # coord pdb
> coordpdb parts/fixed_${i}.pdb PRO$i
>
> regenerate angles dihedrals
>
> }
>
> regenerate angles dihedrals
>
> writepdb KcsA_ester.pdb
> writepsf KcsA_ester.psf
>
>
> -----------------------------------------------------------------------------------------------
>
>
>
> The resulting pdb has both the OE atom and the HA atom of the
> Tyr78-Gly77 ester are failed to be guessed. My current solution to fix the
> atoms OE position it so move the atom using scripting is to move that atom
> to the crystal structure atom position. I am worried that this is will
> induce artifacts however. My only other thought is build a separate top
> file for TYF residue in 4MSW from the protein topology/parameters and the
> top of the patch. Any advice is welcome, and thanks for your time.
>
>
>
> Kyle
>
> Post Doc. at University of Delaware
>
>
>
>
>
>
>
> --
>
> Josh Vermaas
>
>
>
> vermaasj_at_msu.edu
>
> Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
>
> Michigan State University
>
> vermaaslab.github.io <https://urldefense.com/v3/__http:/vermaaslab.github.io__;!!HXCxUKc!xBR4rlbRRKLv7IGpl3aRcYp3lEhYG9UXX6NNX4FXRM7XOKT5pBke-dN3LGpQ75NJ4VNpEu7-c0c$>
>
>