Hello,
Sorry for not being clear. I have to simulate a DNA bound to a protein.
Usually xleap doesnt recognize the phosphate at the 5' end of nucleic acid.
But i want to consider this 5' phosphate during simulation. All i understand
from previous postings is that i should create a new residue with 5' P and
load its ff and prepin files to make xleap recognize the residue. But i dnt
know how to do it. Could you please write me how can do the same.
Thanks,
Bala
On Tue, Jun 23, 2009 at 9:45 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Bala,
>
> Is there any way to make xleap recognize the 5' phosphate and create the
>> topology.
>>
>
> I am note sure I understand your question. If you want a ff library for the
> 5' phosphate you could use the dimethylphosphate molecule + constraints
> during the fit to generate the corresponding molecular fragment.
>
> regards, Francois
>
>
>
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Received on Mon Jul 06 2009 - 11:00:15 PDT
