[gmx-users] Replacing a molecule with multiple ions

[Mark Abraham]

Hi,

Seems like a straightforward task for the scripting language of your choice
- even grep and sed can do a decent job. Get rid of all but two of the DMA
atoms, change them to whatever ions suit you, and make matching changes to
your [molecules] section manually. You may need to reorder to have all your
lithium atoms together, etc. but there should be no need to renumber
anything.

Mark


On Sun, Jul 6, 2014 at 10:46 AM, Timothy Click <tclick at nctu.edu.tw> wrote:

> Good afternoon from Taiwan. Does anyone know of or have an effective way
> to replace a solvent molecule with multiple ions? For example, I want to
> replace N,N-dimethylacetamide (DMA) with LiCl ions. genion replaces by 1:1.
> I was hoping to replace 1:2 because DMA is large enough that I would prefer
> to replace the position of two different methyl carbons with either a
> lithium or chloride ion.
>
> Thanks.
>
> Cordially,
> 柯明 Timothy H. Click, Ph.D.
> Department of Biological Science and Technology
> Institute of Bioinformatics and Systems Biology
> National Chiao Tung University
> 208 Lab Building 1, 75 Bo-Ai St.
> Dong District, Hsinchu, Taiwan 30062
> (R.O.C.)
> tclick at nctu.edu.tw
>
>
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