On Fri, Jun 21, 2013, Dongshan Wei wrote:
>
> please help me create the .protmp and .inpcrd files for the 2TRX protein
> molecule?
Be sure you understand what you want to do. The only nonstandard parts of TRX
are components of the crystal medium. If you are interested in simulations of
the crystal itself, these are important, but much less so if your simulations
are pointed towards the behavior of thioredoxin in solution.
So, if you are interested in solution simulations, you may not need to do
anything to get going (other than removing unwanted parts from the PDB).
Crystal simulations are specialized tasks, and you will certainly need to gain
a fair amount of experience to attack these. In particular, modeling copper
coordination is a art form, not (to my understanding) amenable to some
"automatic" procedure.
...good luck...dac
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Received on Fri Jun 21 2013 - 06:00:05 PDT
