Dear Pragya,
If you want to continue a previous study (restart a previous simulation
or run a new simulation for direct comparison with previous one), the
best is to use exactly the same force fields you used before. Well,
unless your precise goal is to compare different force fields which is a
different issue ...
Those force fields you used provide already pretty good description for
lots of properties. Although, it always depends what you are after so
its impossible to say if the force fields were good enough for your
question unless we know the question.
However, if you want to start a new study, then you probably also want
to make use of the latest developments and especially improvements for
your particular problem. The AMBER15 manual has a comprehensive
description of new force fields for different biomolecules at pages
30-40. I think if you read those pages plus if you read the literature
where the modifications were published you should get a good idea how to
choose your force field.
Best wishes
Vlad
On 08/05/2015 09:35 AM, Pragya Priyadarshini wrote:
>
>
> Dear Amber users,
>
> I have to do MD simulation of protein-DNA complex, earlier I have used
> ff99SB + bsc0 force field of AMBER11, now I have to use AMBER 14 for my
> study. For protein, it is mentioned in AMBER14 manual, to use ff14SB but
> I am not getting about DNA. Is ff14SB, sufficient for DNA of protein-DNA
> complex or I have to other force field.
>
> Please suggest me.
>
> Regards
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
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Received on Wed Aug 05 2015 - 01:30:02 PDT
