Re: regarding protein-dna complex simulation

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Dec 19 2008 - 19:53:28 CST

Dear Prasun,

On Fri, Dec 19, 2008 at 7:47 PM, prasun kumar <prasun30_at_gmail.com> wrote:
> Respected all
>
> I am trying to simulate a protein dna complex.For this I run a separate
> simulation for protein and DNA(I know its not a right method,but its a test
> only because i am a beginner).For protein its running fine but for DNA I am
> getting error which is folowing:
>
> FATAL ERROR: CAN'T FIND DIHEDRAL PARAMETERS FOR HN8 CN8 CN7B NN3A
>
> then I enquired Inp file and prm file I found that there is not such type of
> dihedrals forming I have used the patches DEO1 for C,T and DEO2 for G,A and
> 3pho &5ter.Can any one suggest me where I am going wrong?

Which parameter file did you use?

Cheers,
Leo

-- 
Leonardo Trabuco, Ph.D. candidate
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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