Hello all
I have modeled a protein using MODELLER9v8 and a B-DNA using amber module NAB.
When I modeled DNA by NAB TER card was added itself between two strand.
Both structure were docked in HADDOCK server.
When I ran MD simulation of docked complex, in first step of minimization
(minimization of solvent + ions)complex was OK but in second step of minimization
(minimization of protein)two ends of DNA become bonded to eachother.
When I checked the PDB generated after docking TER card was removed between two DNA
strand and both strand were of same chain name. so I think these are the reasons
for
bonding of two strand during minimization.
So can anybody sugest me how to resolve this.
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Thu Dec 16 2010 - 23:00:05 PST
