[AMBER] Atom selection for restraints

From: Date, Mihir <Mihir.Date.STJUDE.ORG>
Date: Mon, 29 Oct 2012 17:41:10 -0500

I want to restrain all atoms except hydrogen for my first minimization of protein and two ligands complex in vacuum.

Following is my input for sander.

        imin = 1,
        MAXCYC = 500
        ncyc = 250,
        ntb = 0,
        igb = 0,
        cut = 999,
        ntr = 1,
        restraintmask=:* & !.H=

sander -O -i minimize.in -o mini_vaccu.out -p complex.prmtop -c complex.inpcrd -r complex_vaccu.rst -ref complex.inpcrd

it gives me message

Cannot match namelist object name .*
namelist not terminated with / or &end

When I looked into output file, the restraints energy is 0.0000 and no atoms are selected for restraints.

Frozen or restrained atoms:
     ibelly = 0, ntr = 1
     restraint_wt = 500.00000

and in energy table
RESTRAINT = 0.0000

The sytax I used for atom selection is exactly as shown in Amber12 manual (page 320). My input pdb has hydrogen present.
How I can select only heavy atoms and exclude all hydrogens from restraints?
Is there any mistake in my syntax for atom selection?

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Received on Mon Oct 29 2012 - 16:00:03 PDT
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