you can use the restraintmask syntax, here is an example for all atoms
except water and hydrogens:
ntr=1, restraintmask="!:WAT & !.H=", restraint_wt=100.0
On Sun, Jun 23, 2019 at 2:49 PM James Starlight <jmsstarlight.gmail.com>
wrote:
> 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 Mon Jun 24 2019 - 04:30:02 PDT
