HI Rana,
If you have docked the protein fragments and they are in two different pdb files then you can simply load them in leap.
Using the "combine" keyword you can make a single coordinate file and do the necessary processing to save your parameter and topology file for your simulations.
YOu can also use "savepdb" keyword to save the single pdb file of those combined fragments (previously done using "combine")
Is this what you wanted to do?
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: Rana Rehan Khalid <rrkhalid.umich.edu>
Sent: 21 September 2017 01:15
To: AMBER Mailing List
Subject: Re: [AMBER] simulation of docked domains of protein
Hi, Our system consist of two fragments, one have 324 residues while
other fragment consist 43 A.A residues. I want to study the conformation
changes when the smaller fragment of amino acids docked with the larger
fragment. how i manage these two fragment in the single pdb file.
Regards
On Wed, Sep 20, 2017 at 9:36 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> The nature of simulations will depend on what exactly you want to study.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: Rana Rehan Khalid <rrkhalid.umich.edu>
> Sent: 20 September 2017 21:56
> To: AMBER Mailing List
> Subject: [AMBER] simulation of docked domains of protein
>
> Hi everybody
>
> I docked the two domains of protein and want to study the simulation of
> docked domain is there any tutorial to deal with such kind of simulation
>
> Thanks.
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>
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Received on Wed Sep 20 2017 - 23:30:02 PDT
