VMD-L Mailing List

From: Josh Vermaas (vermaasj_at_msu.edu)
Date: Mon Mar 25 2024 - 15:01:52 CDT

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!8GlYHbB2PFC3Nm3ypkOEG25_UwyAVBXVT5iGTqsMHNhVb4_w_J1BovVi127OD3SyPpco0cZXPSrFHqKfh28$
> <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