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Hello friends,<br>
<br>
I am trying to simulate a protein of 36 residues (HBD1) in water .
Since my protein has net charge of <br>
+4 I had to neutralize it by adding 4 chlorine ions using ' genion'.
After that I edited the .top file to add the required <br>
"ions.itp" and also reduced the number of SOL molecules by 4 in the [
molecules ] line and added one line for Cl 4 <br>
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 ...<br>
The following are the sequence of commands I give:<br>
<br>
<b>pdb2gmx -f HBD1pr.pdb -o HBD1prn.pdb -p HBD1pr.top -ignh<br>
editconf -f HBD1prn.pdb -o HBD1pr_box.gro -c -d 0.6<br>
genbox -cp HBD1pr_box.gro -cs spc216.gro -o HBD1pr_b4em.gro -p
HBD1pr.top<br>
grompp -f em.mdp -c HBD1pr_b4em.gro -p HBD1pr.top -o HBD1pr_em.tpr<br>
genion -s HBD1pr_em.tpr -o HBD1pr_ion.pdb -nname Cl -nn 4 -nq -1 -random</b><br>
I edit the HBDpr.top for including the "ions.itp" and modify the number
of SOL molecules<br>
and also add a line for Cl ions. then delete the HBD1pr_em.tpr file to
create a new tpr file.<br>
<b>rm HBD1pr_em.tpr</b><br>
<b>grompp -f em.mdp -c HBD1pr_ion.pdb -p HBD1pr.top -o HBD1pr_em.tpr<br>
</b><br>
the error is :<br>
<br>
<i>Back Off! I just backed up mdout.mdp to ./#mdout.mdp.41#<br>
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar<br>
checking input for internal consistency...<br>
calling /lib/cpp...<br>
processing topology...<br>
Generated 135 of the 1081 non-bonded parameter combinations<br>
Excluding 3 bonded neighbours for Protein_B 1<br>
Excluding 2 bonded neighbours for SOL 1366<br>
Cleaning up temporary file grompp013645<br>
Fatal error: No such moleculetype Cl<br>
</i><br>
Where am I going wrong I am not able to figure out. Has anybody come
across such problem...please help with suggesions<br>
<br>
sharada<br>
<br>
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