[gmx-users] Unable to add ions...
tsjerkw at gmail.com
Tue Oct 10 09:41:03 CEST 2006
The name depends on the force field used (you didn't mention). You may
need to try CL or CL-
On 10/10/06, sharada <sharada at ccmb.res.in> wrote:
> 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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Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
9747AG Groningen, The Netherlands
+31 50 363 4336
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