Re: regarding protein-dna complex simulation

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Dec 19 2008 - 20:16:04 CST

Can you describe how you built your system in detail? Please post the
script in case you used one.

Thanks,
Leo

On Fri, Dec 19, 2008 at 8:11 PM, prasun kumar <prasun30_at_gmail.com> wrote:
> top_all27_prot_na.rtf and par_all27_prot_na.prm
> I tried with RNA also,its not giving any error.......
> thanx for your reply
>
> On Sat, Dec 20, 2008 at 7:23 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
> wrote:
>>
>> 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
>
>
>
> --
> PRASUN (ASHOKA)
>

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

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