Can I use dielectric constants specific to the type of residue with gmx_MMPBSA?

[narubi2]

Hi all.

I found some articles suggesting to use residue type specific dielectric constants instead of one dielectric constant for all residues (https://pubs.acs.org/doi/10.1021/acs.jcim.8b00248).
The effect of using residue type specific dielectric constants might depend on the type of protein or ligand. But I think it is worth a try.

Any suggestions or advice would be greatly appreciated.

[marioernestovaldes]

you can adjust the dielectric constant based on residues with the cas_intdiel variable: https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/input_file/#alanine_scanning-namelist-variables

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On Tue, Mar 19, 2024 at 2:43 AM narubi2 ***@***.***> wrote: Hi all. I found some articles suggesting to use residue type specific dielectric constants instead of one dielectric constant for all residues ( https://pubs.acs.org/doi/10.1021/acs.jcim.8b00248). The effect of using residue type specific dielectric constants might depend on the type of protein or ligand. But I think it is worth a try. Any suggestions or advice would be greatly appreciated. — Reply to this email directly, view it on GitHub <#474>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALDMPHJQN5BCB4LLCMJQO2LYY73DLAVCNFSM6AAAAABE5C3UAOVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZWGM4TIMJZG4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[narubi2]

Oh, I didn't know 'cas_intdiel' variable.
Thanks you @marioernestovaldes