Using XML Ligand Parameter Files with openmmdl for Protein/Membrane Simulations

[mmagithub]

Hi,

I’d like to confirm whether openmmdl can support ligand parameter files provided in XML format (either system.xml or force‑field.xml) for mixed protein or protein–lipid MD simulations. My ligand parameters are supplied only as an XML file (example attached), and neither interchange nor ParmEd appears able to convert them into OFFXML or AMBER‑compatible formats.

Could you let me know if there is a current workflow—or an upcoming feature—that would allow these XML parameters to be used directly?

Thank you for your help.

Best regards,
Marawan

thiazo-phenyl.pdb.txt
thiazo-phenyl.sdf.txt
thiazo-phenyl.xml.txt

[talagayev]

Hey @mmagithub,

Currently OpenMMDL does not support the conversion or input of .xml/.offxml files.
For the conversion from .xml to .offxml probably openforcefield people would be more knowledgeable how to do this, as for the support of direct input of .offxml we can add it into OpenMMDL if this would be of your interest.

Best,
Valerij

[mmagithub]

Thanks Valerij.

I believe this would be a good addition (I mean allow using offxml, or gromacs itp/top as well), especially this is how tools like bespokefit provides their parameter outputs.

Thanks

[talagayev]

Hey @mmagithub,

Looked quickly into how possible it is to do it. From the first look the .offxml it should be doable, would be similarily porbably to this tutorial, with then the .offxml of the ligand from bespokefit being then combined with the .offxml for the protein, so the parameterization is connected.

I would look into it and ask Matt/Jeffreý who are more familiar with how reasonable that approach would be and try to implement it. If my assumption is correct the code modification won't be that much and the feature should be implemented quickly.

Best,
Valerij

[mmagithub]

That would be awesome, especially if it can also work with amber19sb and be able to handle the new CMAP issues in this FF.

Thanks