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tristanic / isolde

Interactive molecular dynamics based model building into low-resolution crystallographic and cryo-EM maps
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Heparin #15

Closed xuewuzhang-UTSW closed 1 month ago

xuewuzhang-UTSW commented 10 months ago

Dear Tristan, Is it possible to simulate heparin chains (not covalently linked to any protein) with ISOLDE? When I tried it with ISOLDE in ChimeraX, it complained that the glycan residues (SGN and IDS, which are standard names for the two residues in heparin in the PDB database) are not parametrized. I guess it is probably not currently available, but wonder if there is a way to create custom parameter xml files. I have tried to use the LigParGen server to generate the xml files for the two residues and load them into ISOLDE, but there were several issues that made them not work. It complained that "Found multiple NonbondedForce tags with different 1-4 scales". At one point I was able to parameterize one SGN residue at one terminal, but failed for residues in the middle. I guess that a patch is needed to deal with the bond formation and atom removal when the residue is in the middle of a chain, but don't know how to do it. Thanks, Xuewu

Guillawme commented 3 months ago

Hi!

It's a bit late to answer maybe, but I will post anyway in case it is helpful.

Have you tried directly within ISOLDE? It can't parameterize metal complexes, but works fine with organic molecules. Here is how to do it from a fresh ChimeraX session:

  1. open your molecule
  2. start ISOLDE
  3. set your molecule as the working model in ISOLDE
  4. select the whole molecule
  5. if it doesn't have hydrogens, run addh sel
  6. in ISOLDE's "General" tab, open "Residue Parameterisation" and click the "Parameterise residue" button (see screenshot)
  7. when it completes (it takes a few minutes), the XML file will be written to the directory from which you started ChimeraX

When you need to use the new parameter file, load it by clicking on the "Load residue parameters" button in the same section. You will need to load the parameter file each time you restart ChimeraX.

I hope this helps!

Screenshot from 2024-05-28 16-47-16

xuewuzhang-UTSW commented 3 months ago

Hi Thanks for the tips. Tristain has made updates to ISOLDE to make it able to handle heparin. Parameterization within ISOLDE works for small ligands, but it cannot do long chain heparin with many atoms. Xuewu

On Tue, May 28, 2024 at 9:55 AM Guillaume Gaullier @.***> wrote:

Hi!

It's a bit late to answer maybe, but I will post anyway in case it is helpful.

Have you tried directly within ISOLDE? It can't parameterize metal complexes, but works fine with organic molecules. Here is how to do it from a fresh ChimeraX session:

  1. open your molecule
  2. start ISOLDE
  3. set your molecule as the working model in ISOLDE
  4. select the whole molecule
  5. if it doesn't have hydrogens, run addh sel
  6. in ISOLDE's "General" tab, open "Residue Parameterisation" and click the "Parameterise residue" button (see screenshot)
  7. when it completes (it takes a few minutes), the XML file will be written to the directory from which you started ChimeraX

When you need to use the new parameter file, load it by clicking on the "Load residue parameters" button in the same section. You will need to load the parameter file each time you restart ChimeraX.

I hope this helps!

Screenshot.from.2024-05-28.16-47-16.png (view on web) https://github.com/tristanic/isolde/assets/9656546/2b718e2d-4f6b-446e-8737-ba8836e9cdaf

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