Dear Jane,
Sorry for misleading you. In fact, we are not interested in the simulated RNAs. In stead, we use GB model just for a comparison to our model, so it is the performance we really concern. Thanks a lot!
Best,
Yufeng
At 2013-04-27 12:08:50,"Jian Yin" <janeyin600.gmail.com> wrote:
>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 - 22:00:02 PDT
