Re: regarding protein-dna complex simulation

From: Leonardo Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Fri Dec 19 2008 - 20:44:16 CST

Please keep the discussing in the namd-l list.

The first thing I'd do is renumber your residues so that you don't
have negative resids. This may not be the cause of your current
problem, but will be the cause of some future problems. You may need
to move your coordpdb statement before the patches. It's also
advisable to add a 'regenerate angles dihedrals' after patches are
applied.

Another question: do you really want to rewrite your input file? You
are using the same file name for your input and your output PDB.

I would recommend that you build a simpler system first to understand
how the process work. You can for instance work on a few residues from
your DNA molecule and make sure you get that right. You should always
load your .psf and .pdb files in VMD and visually inspect it.

Cheers,
Leo

On Fri, Dec 19, 2008 at 8:20 PM, prasun kumar <prasun30_at_gmail.com> wrote:
> Actually I have PDB file 1kx5.I have taken it for my simulation.
> I have done the following changes:
> DT-THY
> DA-ADE
> DC-CYT
> DG-GUA
> OP1-O1P
> OP2-O2P
> C7-C5M
> 1kx5 is having 146 nucleotides.so I have used the patches accordingly for
> purine and pyrmidines
> I am attaching my *.pgn file also please have a look.
>
> On Sat, Dec 20, 2008 at 7:46 AM, Leonardo Trabuco <ltrabuco_at_ks.uiuc.edu>
> wrote:
>>
>> 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
>
>
>
> --
> PRASUN (ASHOKA)
>

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

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