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Support for other forcefields like AMBER #31
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- Hi Marawan, You are right, the implementation of a different forcefield requires re-coding of the process, we have on the pipeline to do so to include pipelines for CHARMM and AMBER, but we are short on personal and current funding os not allocated for this project, still we are working on the side to advance on this sense, will keep the community posted, thanks for reaching out! Best Hugo ------------------------------------------- Hugo Gutierrez de Teran, PhD. Professor in Computational Biochemistry Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-751 24 Uppsala (SWEDEN) Phone: +46(0)18 471 5056 e-mail: ***@***.******@***.***> GPCR-ModSim: www.gpcr-modsim.org<http://www.gpcr-modsim.org/> Group Leader in Computational Biochemistry CINN / CSIC Health Institute of Principado de Asturias, Oviedo (Spain) ------------------------------------------- On 30 Mar 2025 at 01:40 +0100, mmagithub ***@***.***>, wrote: Nice repo, thanks. Wondering if it is possible to provide other protein and / or lipid forcefields to pymemdyn, as it looks like it is only OPLS that is supported and hard coded. Thanks, Marawan — Reply to this email directly, view it on GitHub<#31>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABU6HHTTF7LTSIP6255ALBT2W44PHAVCNFSM6AAAAAB2B47LJ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2TQNJYGI2DGMA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [mmagithub]mmagithub created an issue (GPCR-ModSim/pymemdyn#31)<#31> Nice repo, thanks. Wondering if it is possible to provide other protein and / or lipid forcefields to pymemdyn, as it looks like it is only OPLS that is supported and hard coded. Thanks, Marawan — Reply to this email directly, view it on GitHub<#31>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABU6HHTTF7LTSIP6255ALBT2W44PHAVCNFSM6AAAAAB2B47LJ2VHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2TQNJYGI2DGMA>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policyReacted by mmagithub
I see, thanks.
Since this is still a work in progress, it would be great to see support for additional small molecule force fields beyond LigParGen. For example, allowing users to supply their own SDF/PDB and parameter files would be very beneficial. Many thanks in advance!
- Hi Marawan, This is possible, through only on the command-line version (i.e. no longer possible on the web server), please refer to the manual and if you still have doubts don’t hesitate to contact me again. This said, if you are using the Berger lipid parameters and OPLSFF for the protein, I am afraid that Ligpargen (or alternatively fold from Schrödinger if you have that) generated OPLS parameters for the ligand are the only compatible with the rest of the setup, i.e. mixing forcefields otherwise is quite delicate. Best, Hugo ------------------------------------------- Hugo Gutierrez de Teran, PhD. Professor in Computational Biochemistry Department of Cell and Molecular Biology Uppsala University BMC, Box 596 SE-751 24 Uppsala (SWEDEN) Phone: +46(0)18 471 5056 e-mail: ***@***.******@***.***> GPCR-ModSim: www.gpcr-modsim.org<http://www.gpcr-modsim.org/> Group Leader in Computational Biochemistry CINN / CSIC Health Institute of Principado de Asturias, Oviedo (Spain) ------------------------------------------- On 30 Mar 2025 at 23:06 +0200, mmagithub ***@***.***>, wrote: I see, thanks. Since this is still a work in progress, it would be great to see support for additional small molecule force fields beyond LigParGen. For example, allowing users to supply their own SDF/PDB and parameter files would be very beneficial. Many thanks in advance! — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABU6HHVI3PG7HW5ZYKQG2ND2XBMGJAVCNFSM6AAAAAB2B47LJ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUG42DKOBRGA>. You are receiving this because you commented.Message ID: ***@***.***> [mmagithub]mmagithub left a comment (GPCR-ModSim/pymemdyn#31)<#31 (comment)> I see, thanks. Since this is still a work in progress, it would be great to see support for additional small molecule force fields beyond LigParGen. For example, allowing users to supply their own SDF/PDB and parameter files would be very beneficial. Many thanks in advance! — Reply to this email directly, view it on GitHub<#31 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABU6HHVI3PG7HW5ZYKQG2ND2XBMGJAVCNFSM6AAAAAB2B47LJ2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDONRUG42DKOBRGA>. You are receiving this because you commented.Message ID: ***@***.***> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
Nice repo, thanks.
Wondering if it is possible to provide other protein and / or lipid forcefields to pymemdyn, as it looks like it is only OPLS that is supported and hard coded.
Thanks,
Marawan