Re: peptides on surface

From: Roman Petrenko (rpetrenko_at_gmail.com)
Date: Wed May 13 2009 - 17:30:00 CDT

Jorgen, just out of curiosity, do you have original pdb file with
coordinates of your peptides? If not, how are you generating
structures from the sequence?

On Wed, May 13, 2009 at 6:02 PM, Eduardo Cruz-Chu <chucruz_at_ks.uiuc.edu> wrote:
> Look at this reference:
>
> Rosemary Braun, Mehmet Sarikaya and Klaus Schulten. Genetically engineered
> gold-binding polypeptides: structure prediction and molecular dynamics.
> Journal of Biomaterials Science, Polymer Edn. 13, 747-757 (2002)
>
>
>
> On Wed, 13 May 2009, Jorgen Simonsen wrote:
>
>> Hi all,
>>
>> I would like to simulate 10 peptides and their interactions on a silver
>> surface - I am not too interested in the beginning to simulate quantify
>> the
>> interaction from the surface. I am planning to simply freeze the surface
>> atoms and add a vdw potential to them as I am mainly interested in the
>> peptide interactions in the beginning. I have not been able to find any
>> papers using namd for this - has anybody tried?
>>
>> Thanks in advance
>>
>> Best
>>
>> Jorgen
>>
>
>

-- 
Roman Petrenko
Physics Department
University of Cincinnati

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