[gmx-users] Fw: MDsimulation of Protein-DNA complex

soumi soumi90 at rediffmail.com
Tue May 3 15:56:40 CEST 2016

From: "soumi "<soumi90 at rediffmail.com>Sent: Tue, 03 May 2016 19:21:47To: <gmx-users at gromacs.org>Subject: MDsimulation of Protein-DNA complexDear All,             I am working on MDsimulation of Protein-DNA complex using AMBER99SB-ILDN force field with gromacs.In order to neutralize the net charge on the protein-DNA complex by adding the correct number of  positive ions or negative ions  I have used the following command in gromacs 
gmx genion -s ions.tpr -o  solv_ions.gro -p topol.top -pname NA -nname CL -np 38
When prompted, I choose group 13 "SOL" for embedding ions because I do not want to replace parts of protein-DNA complex with ions.In MM  optimisation process for solvated complex,counter ions are easily separated from the solute .Such separated ions have no function as a counter ion.In order to avoid such situation I desire the positions of Na+ ions around DNA to be constrained within 5 A from the PO4- groups of DNA backbone,while the Na+ ions around protein were contrained within 6 A from the  carbon atom of the carboxyl group of the negatively charged Asp 129 residue.How can the positions of Na+ ions around DNA be constrained within 5 A from the PO4- groups of DNA backbone by which command or method using  gromacs exclusively (not AMBER TOOL /AMBER PACKAGE )?With Regards ,Soumi Das

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