Ok, thank you!
p.s. are there utility in amber-tools, which may indicate number of
standard amino acids in protein?
m.b. quite usefull with (:1-${seq})&(.CA,C,O,N)
where seq is the number of last residue :-)
пн, 24 июн. 2019 г. в 14:12, David A Case <david.case.rutgers.edu>:
>
> 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 - 06:00:09 PDT
