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

[David van der Spoel]

Peggy Yao wrote:
> 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. 
try with position restraints on protein and Ca2+ and without water first.

>  
> Many thanks for any help..
>  
> Peggy
>  
>  
> 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 -norandom
> 
> 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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se