[gmx-users] Re: gro does not match top

[Justin Lemkul]

On 3/24/13 9:02 AM, Shima Arasteh wrote:
> In fact the genion does not add the neutralizing CL ions to gro file! Why?
> How can I solve this problem?
>

Using -nn and -conc is probably incompatible, because -conc will add some number 
of ions, which may not play nicely with the fact that you are then manually 
saying "add only 3 negative ions" with -nn 3.  The correct formation of the 
command is to use genion -conc 1 -neutral.

-Justin

>
>   Would you please help me?
>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Shima Arasteh <shima_arasteh2001 at yahoo.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Sunday, March 24, 2013 5:16 PM
> Subject: gro does not match top
>
>
>
> Hi,
>
> I am solving a protein in water. This protein has a charge of +3.
> After solvation there is 3272 water molecules.
>
> Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system.
> #genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1
>
> After this, the top file shows:
>   Protein_chain_A     1
>
> SOL         3147
> NA               61
> CL               61
> CL               3
>
> But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error.
> What' s your suggestions? How does it come?
>
> Thanks in advance.
>
>
>
> Sincerely,
> Shima
>

-- 
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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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