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I think this arises from using the outdated leaprc file: the MG atom type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 - 12:30:02 PDT
