You need to learn to use a molecular editor to make and study
conformations, in order to make an initial model. xleap could be used in
a pinch, but others that I am unfamiliar with are more popular. Using
another program, you would save a pdb file with both molecules, the use
loadpdb in leap to begin turning it into amber input files.
Bill
On 9/20/17 12:45 PM, Rana Rehan Khalid wrote:
> 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 - 13:00:04 PDT
