Re: Add ions/molecules different from Autoionize defaults

Date: Fri Dec 25 2015 - 07:16:46 CST


Hi. Packmol might be of help too.



On 2015-12-24 20:15, Peter Freddolino wrote:

> Hi Ardavan,
> The easiest way is probably just to build the molecule you want as a pdb file, and scatter the desired number of copies as appropriate in your system prior to running psfgen.
> Best,
> Peter
>> On Dec 24, 2015, at 8:37 AM, Ardavan Mehdizadeh <> wrote: Hi, I was wondering if someone could help me with adding other ions and molecules in protein and water box system to a certain concentration; ions and molecule which are not available in VMD>Autoionize. Something like, Sodium Acetate or some molecules like Mannitol (Manna Sugar). Thanks.


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