[gmx-users] Re: Fwd: How to can i replace a molecule

[shika]

Thanks Justin.

May I ask something, if i'm using the command for genbox before
minimization which is

genbox -cp protein_box.gro -cs solvent.gro -p control.top -o prot_solv.gro

next i insert water by using same command;

genbox -cp prot_solv.gro -p control.top -cs spc216.gro -o
prot_solv_wtr.gro maxsol 350

i'm using -cs for both genbox command instead of -ci -nmol, is it
wrong to use the command like that?




On Mon, Oct 8, 2012 at 8:59 AM, Justin Lemkul [via GROMACS]
<ml-node+s5086n5001764h68 at n6.nabble.com> wrote:
>
>
> On 10/7/12 3:52 PM, Ali Alizadeh wrote:
>> Dear All users
>>
>> How to can i replace a molecule(for example methane) with another
>> molecule(propane)?
>> Number of these molecules are given and their position is random,
>>
>> Can I use genbox or genion, How to do i do it?
>>
>
> Likely you can't, as you were already advised:
>
> http://lists.gromacs.org/pipermail/gmx-users/2012-October/075338.html
>
> A more robust approach for dealing with mixed systems can be found here:
>
> http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents
>
> -Justin
>
> --
> ========================================
>
> 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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-- 
Best Regards,

Nur Syafiqah Abdul Ghani,
Theoretical and Computational Chemistry Laboratory,
Department of Chemistry,
Faculty of Science,
Universiti Putra Malaysia,
43400 Serdang,
Selangor.
013-7188131
alternative email : syafiqahabdulghani at gmail.com




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