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

[Dallas Warren]

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(CH3NH
2),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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