On Sun, Jun 23, 2019, James Starlight wrote:
>
>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);
I have to ask if you have really read Chap. 19 of the Reference Manual?
This seems to cover all of the questions you have above. Don't be
shy about running experiments: the "ambmask" utility allows you to
provide test atom-expressions and see exactly which items are chosen.
....dac
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Received on Mon Jun 24 2019 - 05:30:05 PDT
