Free Energy calculation on part of the molecule

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1

GROMACS version:
GROMACS modification: Yes/No
Hello guys,
I’m trying to do a FE calculation that set lambda for the palmitoylation on two residues of membrane protein, but cannot make it through.
I generated an .ndx , and set mdp options couple-moltype = CYSP which is the name of palmitoylated residue in .ndx file.
The error shows ‘Did not find any molecules of type ‘CYSP’ for coupling’.
It seems that the .top needs to include the [moleculetype]. Simply adding CYSP to .top could not help of course, as no .itp for CYSP is attached.
Thank you @jalemkul for the answer before.
Are you talking about defining a Protein A with palmitoylation and a Protein B without palmitoylation in the .top?
I’m not sure how to realize ‘relative FE calculation’ you mentioned. What are the crucial steps or options of it which are different from the tutorial?

Thank you all.

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Hi,

just a commend to avoid confusion. CYSP is the name of a residue of your protein. [moleculetype] in the topol.top define the molecules included in the system. I guess in your case will be Protein, SOL, etc. The option couple-moltype in mdp ask for a molecule.

Best regards
Alessandra

3

The approach for a relative free energy calculation is somewhat different.

You need to include dummy atoms in your coordinates and topology for the atoms that will “appear” in the course of the transformation, and manually edit the topology to include A- and B-states for any atom whose properties will change.

In the .mdp files, you do not use couple-moltype, couple-lambda0, or couple-lambda1. Those are only for absolute free energy calculations.

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