[AMBER] error in MD of modeled & docked protein - DAN complex

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Thu, 16 Dec 2010 14:52:38 +0530 (IST)

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
bonding of two strand during minimization.

So can anybody sugest me how to resolve this.

With regard
Sangita Kachhap

AMBER mailing list
Received on Thu Dec 16 2010 - 23:00:05 PST
Custom Search