[MMTK] Nucleotide Sequences, Solvation question

Justin Lemkul jalemkul at vt.edu
Wed Mar 30 17:09:38 CEST 2005

Hello all,

Thanks to all for the help in getting MMTK running.  It is functioning 
beautifully now.  
Thanks Konrad, for a great tool.  I have been working mostly with proteins, 
and would 
like to examine some short nucleotide sequences of my own creation.  I am 
trying to mirror Amber functions within MMTK (construction of small systems of 
nucleotides/peptides, etc.)  I was reading up about how to construct a 
nucleotide chain, 
but I can't seem to get the syntax right.  Can someone show me how to create, 
example, a very short chain of, say, CAGT?

Also, is there a capability within MMTK of adding counterions on a charged 
molecule?  This also goes back to trying to replicate Amber, where counterions 
could be 
added to neutralize charge before solvating, etc.



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