[gmx-users] Unable to add ions...

sharada sharada at ccmb.res.in
Tue Oct 10 09:36:13 CEST 2006

Hello friends,

I am trying to simulate a protein of 36 residues (HBD1) in water . Since 
my protein has net charge  of
+4  I had to neutralize it by adding 4 chlorine ions using ' genion'. 
After that I edited the .top file to add the required
"ions.itp" and also reduced  the number of SOL molecules by 4 in the [ 
molecules ] line and added one line for  Cl     4 
to complete the top file. After this when I run the grompp program with 
the new pdb file containing the ions. However it is not able to 
recognize the Cl ions ...
The following are the sequence of commands I give:

pdb2gmx -f HBD1pr.pdb -o HBD1prn.pdb -p HBD1pr.top -ignh
editconf -f HBD1prn.pdb -o HBD1pr_box.gro -c -d 0.6
genbox -cp HBD1pr_box.gro -cs spc216.gro -o HBD1pr_b4em.gro -p HBD1pr.top
grompp -f em.mdp -c HBD1pr_b4em.gro -p HBD1pr.top -o HBD1pr_em.tpr
genion -s HBD1pr_em.tpr -o HBD1pr_ion.pdb -nname Cl -nn 4 -nq -1 -random
I edit the HBDpr.top for including the "ions.itp" and modify the number 
of SOL molecules
and also add a line for Cl  ions. then delete the HBD1pr_em.tpr file to 
create a new tpr file.
rm HBD1pr_em.tpr
grompp -f em.mdp -c HBD1pr_ion.pdb -p HBD1pr.top -o HBD1pr_em.tpr

the error is :

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_B           1
Excluding 2 bonded neighbours for SOL              1366
Cleaning up temporary file grompp013645
Fatal error: No such moleculetype Cl

Where am I  going wrong  I am not able to figure out.  Has anybody come 
across such problem...please help with suggesions


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