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Add parameters to allow covalent docking to Serine #757

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amjjbonvin opened this issue Dec 12, 2023 · 0 comments
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Add parameters to allow covalent docking to Serine #757

amjjbonvin opened this issue Dec 12, 2023 · 0 comments
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community contributions from people outside the haddock team enhancement Enhancing an existing feature of adding a new one parameters-topologies Issues/feature requests related to the force field

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@amjjbonvin
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A user mentioned he would like to perform covalent docking to SER residues.
We have parameters for CYC (a modified CYS with reduced van der Waals parameters on the SG atom).

Describe the solution you'd like

Similarly to CYS, we should create a special topology for a SER with reduced vdw parameters on the side chain oxygen and lacking the OH hydrogen.
@amjjbonvin amjjbonvin added parameters-topologies Issues/feature requests related to the force field user-driven labels Dec 12, 2023
@amjjbonvin amjjbonvin self-assigned this Dec 12, 2023
@rvhonorato rvhonorato added community contributions from people outside the haddock team enhancement Enhancing an existing feature of adding a new one and removed user-driven labels Dec 13, 2023
@rvhonorato rvhonorato linked a pull request Dec 19, 2023 that will close this issue
Implemented SEC residue for covalent docking #761
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amjjbonvin added a commit that referenced this issue Jan 16, 2024
@amjjbonvin
implement Serine for covalent docking (SEC) - issue #757
4916a6b
amjjbonvin added a commit that referenced this issue Jan 18, 2024
@amjjbonvin
Merge pull request #788 from haddocking/covalSER
4dad36f 
Add topo/params for covalent docking Serine (SEC) - issue #757
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community contributions from people outside the haddock team enhancement Enhancing an existing feature of adding a new one parameters-topologies Issues/feature requests related to the force field
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Implemented SEC residue for covalent docking haddocking/haddock3
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@amjjbonvin @rvhonorato