Hi,
For sure you have to minimize the protein structure (and the solvent, if
present), before to attempt MD simulations.
For a similar system (protein-DNA) I've succesfully used ff99SB for
nucleic acids and ff03 for the protein, modified with Zn-binding
parameters [Mori M et al., J Chem Inf Model. 2010 Mar 4. (Epub ahead of
print)]. Just load both of them in leap module.
About the version of Amber, I've used without problems AMBER10. I think
the MMPBSA test problem has been already fixed, check the archive.
However Amber9 should also works fine.
Regards
Mattia
geyan ha scritto:
> Hi all amber users,
> I want to do MD about a system of proteins and DNA complex. Before the MD,I think the first step is to minimize the protein 3D structure which is produced by homology modelling.
> My question is choosing which force field for protein,which one for DNA, and which one for the complex?all using ff99SB?
> By the way,amber9 and amber10,which one is better?I have heard of many unexpected problems for amber10 and I met one in MM_PBSA test
>
> --------------
> geyan
> 2010-03-22
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 22 2010 - 06:30:03 PDT
