On Fri, Aug 26, 2011, Jason Swails wrote:
>
> Use parmchk. If you run the program with no arguments, it tells you how to
> use it. By default, it will search gaff.dat and pull out reasonable
> parameters, dumping them to an frcmod file. If there's anything it simply
> *can't* find, it will put a placeholder (all parameters are 0) and say
> "ATTN, need revision". You have to fix those parameters.
Parmchk does a bit more than just look in gaff.dat: it estimates missing
parameters by several algorithms. In its default mode, parameters in gaff.dat
are not put into the frcmod file; parameters it estimates on its own are
output; finally, things it can't figure out get placeholders.
>
> However, I would warn you that gaff dihedrals should not necessarily be
> accepted. Run short simulations to make sure they make sense, as you may
> have to modify some of them by hand.
This is excellent advice.
...dac
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Received on Sun Aug 28 2011 - 06:30:02 PDT
