By the way, ... because this confusion comes up pretty often and
unfortunately it is also in the AMBER manual ...
I'd like to stress that "ff14SB" is a pure protein force field (see
recent papers from Carlos Simmerling's lab).
For DNA the force field is "ff99+bsc0" (the one you used) or adding the
latest modifications "ff99+bsc0+epsOL1+chiOL4" (see table 3.2 in the
AMBER15 manual).
The confusion comes up because the leap files used to load the ff14SB
force field (leaprc.ff14SB, parameter and library files) already contain
the bsc0 modifications for DNA ...
Vlad
On 08/05/2015 10:25 AM, Vlad Cojocaru wrote:
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 05 2015 - 02:00:02 PDT
