[gmx-users] Regarding creating the molecules...

[Dallas Warren]

Here is the link to the GROMACS page was referring to

http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

On 14 Jun 2017 3:40 PM, "Dallas Warren" <dallas.warren at monash.edu> wrote:

> Please keep discussion to the emailing list.
>
> 1/ and 2/ to construct the coordinate file for the molecules, I personally
> use Sybyl or the ATB website, but I'm sure there are many more options out
> there. GROMACS website may have links to some as well.
>
> 3/ not entirely sure what you are asking there.
>
> 4/ was answered in the link I provided in last reply. You do not mix
> forcefields, especially when you are someone with your experience.
>
> Learn to search, using literature databases and Google.
>
> And as stated in last email, read the literature, see what others have
> done, why they used particular forcefields, and decide whether that fits
> with your goals. Don't take the word of some random person on an emailing
> list for this, as it's your research and you have to justify it and ensure
> it is valid for what you want to do.
>
> The GROMACS website has a rough outline on how to perform a simulation, in
> general. Have a read of that, it has all this advice presented in it
> already.
>
>
> On 14 Jun 2017 2:43 PM, "Dilip H N" <cy16f01.dilip at nitk.edu.in> wrote:
>
> Hello,
> 1] Can u kindly tell me how can i create molecules such as Methylamine(CH3
> NH2),Dimethylamine((CH3)2NH), Trimethylamine((CH3)3N),
> TrimethylamineNoxide ((CH3)3NO-).
> 2] are there any software's to create these molecules since i didn't find
> any pdb files for  the above said molecules...
> 3] and what are the changes tht i need to make in the residue names tht
> fit into the specific forcefield....
> 4] how can i simulate the molecules if thy are in different forcefields..??
>
> Thank you..
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student
>
>
>
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