Dear David,
Thank you for your response. Indeed, your work will be appreciated.
I can build the pdb for the cellulose crystal lattice, using its CIF file in Materials Studio. How can I then replicate this structure in three dimensions?
Regards,
Ali
> On 15 Nov 2018, at 20:41, David Cerutti <dscerutti.gmail.com> wrote:
>
> If your structure is amenable to tesselation, then you can use the xtalutil
> programs in AmberTools to do it. See this tutorial:
>
> http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
>
> But, the problem is that you'll need something that's ready to tesselate in
> three dimensions. See if you can find anything in the PDB for this
> problem. I'm working on extensions to cpptraj that will allow you to work
> with all of the independent copies of your asymmetric unit as if they were
> one ergodic unit.
>
> Dave
>
>
> On Thu, Nov 15, 2018 at 2:29 PM Ali Khodayari <
> ali.khodayari.student.kuleuven.be> wrote:
>
>> Dear Amber users,
>>
>>
>>
>> I am trying to build a crystalline cellulose structure in amber. I tried to
>> use "sequence" to build a chain of glucose in tleap using GLYCAM_06j-1
>> force
>> field as follows:
>>
>>
>>
>> cellulose = sequence {ROH 4GB 4GB 4GB 4GB 0GB}
>>
>> set cellulose tail cellulose.6.O4
>>
>>
>>
>> The question is, how can I use this chain to produce a crystal having the
>> lattice parameters of cellulose. In other words, is there a proper way to
>> build a 6*6 structure, using the above-mentioned chain, satisfying the
>> lattice parameters of crystalline cellulose?
>>
>>
>>
>> Thank you in advanced.
>>
>> Kind regards,
>>
>> Ali
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Nov 15 2018 - 13:30:03 PST
