Hi
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.
&cntrl
imin = 1,
MAXCYC = 500
ncyc = 250,
ntb = 0,
igb = 0,
cut = 999,
ntr = 1,
restraint_wt=500.0,
restraintmask=:* & !.H=
/
END
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
