VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 20 2017 - 09:40:20 CDT

Hi Siddharth , as Ashar said there is no single-click solution, but a
decent one is Packmol, which works with plain PDB files.

Giacomo

On Thu, Jul 20, 2017 at 4:23 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> There is no single solution to this problem.
> You can create your own (512 SDS molecule file) or find one already for
> you.
>
> To find one - maybe look at publications? or research groups that do
> similar stuff. Some one might have something in their supplementary to
> offer you.
>
> To make your own - you can do one of two things (or more?):
>
> e.g. I would either take a lipid monolayer/bilayer PDB with 512 lipid
> molecules and replace each of them with the SDS you have.
> or in a vacuum make copies of SDS randomly positioning them as long as
> their is no structural overlap.
>
> I don't see how you can avoid programming. Some solutions exist where you
> can introduce your custom solvent instead of water when solvating a system.
> You could look into that maybe and then delete the SDS molecules exceeding
> your required count.
>
> Maybe wait and someone else might offer a better solution.
>
> Hope this helps.
>
> Best,
> /A
>
> On Thu, Jul 20, 2017 at 6:42 PM, Siddharth Girdhar <
> siddharth.gir47_at_gmail.com> wrote:
>
>> Hi all,
>>
>> I am a beginner to VMD so this is probably a very silly question.
>>
>> What I currently have is a PDB and PSF file for the SDS molecule that I
>> created and I want to solvate 512 of these molecules in a water box.
>>
>> How would I get along with doing that? I know how to get one SDS molecule
>> solvated but how can I add 512 of them together?
>>
>> Thank you,
>>
>> Siddharth Girdhar
>>
>
>
>
> --
> Best,
> /A
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin