Re: [AMBER] Molecular dynamics of tripeptide like organic molecule

From: Petro <>
Date: Wed, 11 Dec 2019 07:19:35 +0100

Have a look on tutorials here:
Run through a couple of them, it will give you a great deal of

Without knowing structure nobody will tell you anything about its
The most straight forward way would be to feed it's PDB structure to PyRED
server and see what output it gives to you. Here is link to it's tutorial

 There is also a tutorial be on parametrization using amber tools.
I hope it will stir you in the right direction.


On Wed, Dec 11, 2019, 05:19 Debasish Mandal <> wrote:

> Dear All,
> I would like to run a molecular dynamics simulation of a
> tripeptide like organic molecule. Could anyone please provide me some idea
> about how I can parametrize and create a box (water box type) of this
> molecules and run MD of the system?
> Many thanks in advance.
> Thanks & Regards
> Debasish
> ======================================
> Debasish Mandal
> Assistant Professor
> School of Chemistry and Biochemistry
> THAPAR Institute of Engineering and Technology,
> Patiala - 147004, Punjab
> India
> E-mail:
> Mob.No-07054948925
> “I’m thankful to all those who said ‘NO’ to me it's because of them, I did
> it
> myself” Einstein
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Received on Tue Dec 10 2019 - 22:30:02 PST
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