AMBER Archive (2007)

Subject: RE: AMBER: Restraintmask syntax

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Dec 04 2007 - 11:44:01 CST

--- Steve Spronk <spronk_at_umich.edu> wrote:

> I don't know of way to select all those atoms, but you could consider not
> worrying about restraining all the hydrogens, since their positions will
> obviously never stray far from their associated heavy atoms (especially if
> you use SHAKE).

I don't use SHAKE because it proved a sensitive minimization on just :77-520,
521. Hope it will work.

  The mask that you'll need to use is
>
> :77-521 | :POP_at_O2,P1,O3,O4,O1,C15,C11,N,C12,C13,C14
>
> Note the syntax of this mask. If I understand your system correctly, in
> your sample mask, you used the "and" character ("&") when you probably meant
> the "or" character ("|").

I want to restraint protein, ligand, and that part of the lipid membrane.
Therefore, it should be "&", if the common meaning of "or" applies.

You also specified selected atom types ("@%")
> when you probably meant selected atom names ("@").

You are right.
Thanks
francesco
>
>
> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
> Francesco Pietra
> Sent: Tuesday, December 04, 2007 10:31 AM
> To: Amber
> Subject: AMBER: Restraintmask syntax
>
> Because of the restriction to 80 characters for restraintmask, I find it
> difficult to accomplish the task for:
>
> 77-520: residue numbers for protein.
>
> 521: residue number for ligand.
>
> POP: residue name for lipid of membrane.
>
> O2, P1, ... : "atom typelist" for a portion of the lipid molecules.
>
> I am not sure that the following is correct syntax, though it will exceed
> the
> allowed number of characters anyway:
>
> ":POP, 77-521 & @%O2, P1, O3, O4, O1, C15, C11, N, C12, H21, H22, H23, C13,
> H31, H32, H33, C14, H41, H42, H43, H11, H12, H51, H52"
>
> Any trick to account for the polar head of POPC? Thanks for help
>
> francesco pietra
>
>
>
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