Dear Amber users!
Performing simulations of protein-sugar complexes using Amber14sb and
GLYCAM parameters, I am using atomic selection based on the numbers of
protein residues as harmonic restraints applied during equilibration.
# example: restrain from 1 to 219 residue;
Group input for protein restraints: 25 kcal/mol.
25.0
RES 1 219
END
How it would be possible to define more general (not assosiated with
the numbering of the suquence) selections based on the amber mask? For
example, I would like to
1) restrain all of the atoms of the system besides the solvent (e.g.
not :WAT and :Na+ :Cl-) with the aim to freeze protein and ligand
during equilibration;
2) restrain all of the protein heavy atoms (indicating types for both
backbone and side-chains);
3) restrain all of the backbone atoms ( which should be selection for
N,C,O as I suppose);
Thank you in advance!
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Received on Sun Jun 23 2019 - 12:00:02 PDT
