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> 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I think this arises from using the outdated leaprc file: the MG atom type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 - 18:00:02 PDT
