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> 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:_e({},
>'cvml', 'crazylyf.126.com');>> 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:_e({}, 'cvml', 'case.biomaps.rutgers.edu');>>
>> 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I think this arises from using the outdated leaprc file: the MG atom type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 - 21:00:02 PDT
