[gmx-users] Add CS ions to system

[Justin Lemkul]

On 5/18/13 10:02 AM, Shima Arasteh wrote:
> Hi all,
>
> I want to add CS ions to my system by genion but it seems impossible when go through the EM.
>
> The molecule section in my top file is:
> Protein_chain_A     1
> Protein_chain_B     1
> POPC        238
> SOL         20406
> NA               681
> CL               702
> CS               19
>
> The commands to neutralize and adding CsCl are as follow:
>
>
> Adding ions:
> #grompp -f ions.mdp -c system_solv.gro -p topol.top -o ions.tpr
> #genion -s ions.tpr -o system_solv_ions.gro -p topol.top -conc 1 -neutral
>
> Adding 19 pairs of CsCl:
>
> #grompp -f ions.mdp -c system_solv_ions.gro -p topol.top -o ions_CsCl.tpr
> #genion -s ions_CsCl.tpr -o system_solv_ions_CsCl.gro -p topol.top -pname CS -np 19 -nname CL -nn 19
>
>
> EM:
>
> And fatal error as I get is:
> #grompp -f minim.mdp -c system_solv_ions_CsCl.gro -p topol.top -o minim.tpr
> Fatal error:
> No such moleculetype CS
>
>
> But I see the CS ion in residuetypes.dat which exist in my directory :
>
> CS    Ion
>
>
> So what's the reason? If it is related to the version of applied GROMACS? I am working with 4.5.5 GROMACS and CHARMM 36 FF.
>

All that residuetypes.dat indicates is that Gromacs, in general, has the ability 
to understand that Cs are ions.  That is not to say that every force field has 
parameters for Cs.  That's your problem - the CHARMM force field you have 
doesn't include parameters for a moleculetype named "CS" (look at its ions.itp 
file), though CHARMM27 packaged with Gromacs does have these parameters.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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