AMBER Archive (2007)

Subject: RE: AMBER: Restraintmask syntax

From: Steve Spronk (spronk_at_umich.edu)
Date: Tue Dec 04 2007 - 10:49:36 CST

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

-----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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