.map and .bnd file formatting for Bedaquilline and out.itp file generation

[ubaidmalik3780-hash]

Dear sir, i have created .map and .bnd file of Bedaquilline but the out.itp file is not satisfying as it is not generating proper itp file , kindly reply with proper formatting logic of .map and .bnd file of bedaquilline and how to choose virtual sites and dihedrals and what exclusions do i need to make in .itp file , it is a humble request

[jag1g13]

Hi @ubaidmalik3780-hash you can see some example .map and .bnd files in the tutorial and in this repository in the tutorials directory and test data directory.

I would recommend drawing out the structure of the molecule by hand and then drawing circles around the atoms you intend to place in the same bead. I found that the easiest way to get started, then refine that to better fit the data. More recently, there have also been some fully automated approaches to mapping, such as in https://pubs.acs.org/doi/10.1021/acs.jcim.4c01874, one of the recent publications from my former supervisor.

I'm afraid I've not worked in molecular modelling for quite a few years now so I don't have any useful advice on virtual sites or dihedrals. I have a vague memory of MARTINI exclusions being only for directly bonded atoms - this seems to be in agreement with a source I was able to find via Google:

[ubaidmalik3780-hash]

Thank you sir for your time and help , just wanted to now if there are any approaches for CG to AA backapping for copolymers and drug complexes

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On Mon, 24 Nov 2025 at 10:54 PM, James Graham ***@***.***> wrote: *jag1g13* left a comment (jag1g13/pycgtool#56) <#56 (comment)> Hi @ubaidmalik3780-hash <https://github.com/ubaidmalik3780-hash> you can see some example .map and .bnd files in the tutorial <https://pycgtool.readthedocs.io/en/latest/tutorial.html> and in this repository in the tutorials directory <https://github.com/jag1g13/pycgtool/tree/main/docs/tutorial_files> and test data directory <https://github.com/jag1g13/pycgtool/tree/main/tests/data>. I would recommend drawing out the structure of the molecule by hand and then drawing circles around the atoms you intend to place in the same bead. I found that the easiest way to get started, then refine that to better fit the data. More recently, there have also been some fully automated approaches to mapping, such as in https://pubs.acs.org/doi/10.1021/acs.jcim.4c01874, one of the recent publications from my former supervisor. I'm afraid I've not worked in molecular modelling for quite a few years now so I don't have any useful advice on virtual sites or dihedrals. I have a vague memory of MARTINI exclusions being only for directly bonded atoms - this seems to be in agreement with a source I was able to find via Google: image.png (view on web) <https://github.com/user-attachments/assets/7b7c28bc-c2ea-4abf-9423-a31fcd477d96> — Reply to this email directly, view it on GitHub <#56 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BXCL3LC3QV3D6CZFBLRQQ2D36M5MBAVCNFSM6AAAAACJA7EO36VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNZRHEYTONZVGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[jag1g13]

The only tool I've ever personally used for backmapping is backward from the MARTINI team, but that was a long time ago. I'm not sure if that's still the preferred method or if there's something better available now.

[jag1g13]

Just having a look back at the code and thinking about updating it, I remembered that PyCGTOOL does include experimental support for backmapping using the mdplus library. I'll try to remind myself how that worked and write up some documentation, but I'm not able to promise a timeline on that - it'll be whenever I manage to find time for it.