Sir,
I run a 15ns simulation of dna-ligand systems(explicit method;
ligand:neutral and have experimental evidence to bind, tried on dna's :at
rich and gc rich systems,
But after a 4-5ns, the ligand strats unbinding and later completely
withdrawn from the dna.
Also the dna rotates about the z axis; which is usually not observed. the
inputs for minimization, heating and production run are all previously used
without any problem. ligand parametrization is done via gaussian and resp
of antechamber. The amber version used is amber11, and ff99bsc0.
Does anyone knows what would have happened? I couldnt find out what would
have gone wrong.
mary varughese
Research Scholar
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Received on Thu May 09 2013 - 02:30:02 PDT
