[gmx-users] Help with energy minimizing protein in water box with CA2+

Peggy Yao peggy.yao at gmail.com
Wed Nov 21 09:05:29 CET 2007

Dear Gromacs users,

Thanks for earlier help on this problem.

I have tried a number of approaches with varying results (all bad,
unfortunately).  I am trying to add two CA2+ ions to my protein (1k9p), but
when I did this genion put the two CA2+ ions very close together and they
flew apart.  Then I tried putting only one CA2+, thinking that it would stay
put.  After I ran an energy minimization, the CA2+ ended up outside of the
box.  Now I am really perplexed.  What could be causing this behavior?  One
thing I haven't tried yet is adding a few CL- ions to make the box neutral
.. somehow I don't feel this is the problem though since I've run
non-neutral analyses before without such disastrous consequences.

Could anyone give me some advice?  I'm at my wit's end.  I am attaching my
script below.  Basically fws_ca.pdb is fine, but fws_b4ion.pdb has CA2+
outside of the water box.  The water in the water box looks like ice cubes
in an ice cube tray, segregated into regular little mini-boxes.  I presume
the latter is a numerical consequence of the CA2+ flying out of the box.

Many thanks for any help..


pdb2gmx -ignh -ff gmx -f 1K9P.pdb -p fws.top -o fws.pdb

# add water
editconf -bt cubic -f fws.pdb -o fws.pdb -c -d 0.9
genbox -cp fws.pdb -cs spc216.gro -o fws_b4em.pdb -p fws.top

# energy minimization
grompp -f minim.mdp -c fws_b4em.pdb -p fws.top -o fws_em.tpr
echo "check 2"
mdrun -v -s fws_em.tpr -o fws_em.trr -c fws_b4ca.pdb -g em.log -e em.edr

# add calcium
grompp -f minim.mdp -c fws_b4ca.pdb -p fws.top -o fws_ca.tpr

echo "12" | genion -s fws_ca.tpr -o fws_ca.pdb -pname Ca -np 1 -g fws_ca.log

awk '{if ($1 == "SOL") {print "Ca  1"; print "SOL 7280"}  else {print $0;}}'
fws.top > temp.top

mv temp.top fws.top

# energy minimization
grompp -f minim.mdp -c fws_ca.pdb -p fws.top -o fws_em2.tpr
mdrun -v -s fws_em2.tpr -o fws_em2.trr -c fws_b4ion.pdb -g em.log -e em.edr
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