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

Tsjerk Wassenaar tsjerkw at gmail.com
Tue Oct 10 09:41:03 CEST 2006

Hi Sharada,

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
>  sharada
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php

Tsjerk A. Wassenaar, Ph.D.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

More information about the gromacs.org_gmx-users mailing list