Hi Yufeng,
I would suggest using the most recent amber force field ff12sb with
explicit solvent model and counterions added to your system. There are lots
of papers on that topic published on good journals you can find. You can
try GB of course but I doubt whether it will perform better than the
explicit model.
Best,
Jane
On Friday, April 26, 2013, wrote:
> Dear Jane,
>
> Thank you very much. Do you have guidelines on GB models and force fields
> with respect to RNA simulation? Should I try all the possibilities?
>
> Best,
>
> Yufeng
>
>
>
>
>
>
> At 2013-04-27 11:24:56,"Jian Yin" <janeyin600.gmail.com <javascript:;>>
> wrote:
> >Hello Yufeng,
> >
> >You might want to be extremely careful on using their results. Unless they
> >came up with very reasonable interpretations on this conclusion, to me it
> >is very likely just a bunch of artifacts added together and they happened
> >to see some "good performance" by coincidence. I would think twice.
> >
> >Best,
> >
> >Jane
> >
> >
> >On Fri, Apr 26, 2013 at 5:51 PM, <crazylyf.126.com <javascript:;><javascript:_e({},
> >'cvml', 'crazylyf.126.com <javascript:;>');>> wrote:
> >
> >> Dear Prof. Case,
> >>
> >> Thank you for your advice. The reason we tried to use the ff98 force
> field
> >> is that a previous paper ("RNA Stability Under Different Combinations of
> >> Amber Force Fields and Solvation Models") concluded a best performance
> for
> >> RNA simulating combining the ff98 and igb1. Currently, we would like to
> >> simulate RNAs implicitly, thus ff98 is one choice.
> >>
> >> Best,
> >>
> >> Yufeng
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> At 2013-04-27 03:08:33,"David A Case" <case.biomaps.rutgers.edu<javascript:;><javascript:_e({},
> 'cvml', 'case.biomaps.rutgers.edu <javascript:;>');>>
> >> wrote:
> >> >On Fri, Apr 26, 2013, crazylyf wrote:
> >> >
> >> >> Besides, I was encountered with another problem. When I tried to
> >> >> generate *.prmtop and *.inpcrd files for a magnesium containing RNA
> >> >> system using leaprc.rna.ff98, errors were returned as follows:
> >> >
> >> >Ouch! Please don't use such old force fields if you can possibly avoid
> >> it!
> >> >The leaprc.rna.ff98 is in the "oldff" directory for a reason: it should
> >> only
> >> >be used if you really need to examine or reproduce old (bad) results.
> >> And you
> >> >will have to know enough to navigate errors that can crop up in files
> >> that are
> >> >15 years old and have not been used for a long time.
> >> >
> >> >> For atom: .R<MG2 76>.A<MG 1> Could not find type: MG
> >> >
> >> >I think this arises from using the outdated leaprc file: the MG atom
> type
> >> >does not have LJ parameters in parm98.dat. With more recent files
> (like
> >> >ions08.lib) there will be an "Mg+" residue that has a MG ion.
> >> >
> >> >...good luck...dac
> >> >
> >> >
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Received on Fri Apr 26 2013 - 21:30:03 PDT
