Dear Mahad,
You are making exactly the confusion I was referring to .... "ff99SB" is
yet another protein-only force field .... I was not referring in any
line of my comment to this force field. Again, everything denoted with
"SB" are protein-only force fields ....
For DNA and RNA, the basic ff is "ff99" (Cheatham et al 1999) (note:
without any "SB"). On top on this, the bsc0 modifications were
introduced. Later modifications for DNA and RNA were separated ...
When loading the leaprc.ff14SB, you load the following: ff14SB for
proteins, ff99+bsc0 for DNA, and ff99+bsc0+chiOL3 for RNA .... So,
although you are loading a file called "ff14SB", you will NOT be using
"ff14SB" for nucleic acids (as again "ff14SB" is a protein-only force
field).
I believe it is quite important that people understand exactly which
force fields precisely their are using when loading a file in leap
Best
Vlad
On 08/05/2015 02:47 PM, Mahad Gatti Iou wrote:
> Dear Vlad,
>
> are you sure that you need to use ff99SB for RNA? I mean, when loading the
> ff14SB using leap this is the output:
>
> Welcome to LEaP!
> Sourcing: /home/mgatti/Scrivania/amber14/dat/leap/cmd/leaprc.ff14SB
> Log file: ./leap.log
> Loading parameters: /home/mgatti/Scrivania/amber14/dat/leap/parm/parm10.dat
> Reading title:
> PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> Loading parameters:
> /home/mgatti/Scrivania/amber14/dat/leap/parm/frcmod.ff14SB
> Reading force field modification type file (frcmod)
> Reading title:
> ff14SB protein backbone and sidechain parameters
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/amino12.lib
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/aminoct12.lib
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/aminont12.lib
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/nucleic12.lib
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/atomic_ions.lib
> Loading library: /home/mgatti/Scrivania/amber14/dat/leap/lib/solvents.lib
>
> It seems that is loading everything. I knew that with this you can use it
> for both protein as well as RNA/DNA since, for instance, I have to analyze
> a protein-nucleic acids complex so I need both force fields.
> Maybe the ff99SB is useful if you have to simulate only a DNA/RNA molecule
> but if it is in complex with amino acids I think it should do the trick
> using the last ones no?
> For me at least the simulations are going properly, pointing out that
> nucleic acids simulations are tough.
>
> Also I found this just by typing "amber rna force field" on google
> (website: http://fch.upol.cz/en/ff_ol/index.php)
> Force Field for RNA
>
> We recommend ff99bsc0χOL3 combination which is well tested. This is
> basically ff99 force field [4] combined with Barcelona bsc0 correction for
> α/γ backbone torsions [5] and a χOL3(= χOL) correction for the glycosidic
> torsion [6,7] which prevents formation of spurious "ladder like" structures
> [6,8]. This combination is present in the ff10, ff12SB and ff14SB force
> fields and is assigned by default by AmberTools 12, 13, 14 and 15 with its
> LEaP based tools.
> Cheers,
>
> Mahad
>
>
> 2015-08-05 10:40 GMT+02:00 Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
> :
>
>> 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
>>
>>
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>>
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--
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 - 06:30:03 PDT
