Hi, I carry on md run on protein-dna complex using
AMBER99SB-ILDN force field. Here I state my
problem. gmx_mpi pdb2gmx -f em267.pdb -o
em267_processed.gro -p topol.top -water tip3p
-ignh it compile
successfully. gmx_mpi
editconf -f em267_processed.gro -o em267_newbox.
VMD tutorial
on Dynamical Network Analysis .Here psf and dcd files have been used to
create the network.My question is :Is it possible to do Dynamical Network
Analysis using VMD through GROMACS trajectories?With Regards,Soumi Das
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he 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
-
From: "soumi "<soum...@rediffmail.com>Sent: Tue, 03 May 2016
19:24:22To: <gromacs.org_gmx-users@maillist.sys.kth.se>Subject: Fw:
MDsimulation of Protein-DNA complexFrom: "soumi
"<soum...@rediffmail.com>Sent: Tue, 03 May 2016 19:21:47To:
<gmx-us...@gro
From: "soumi "<soum...@rediffmail.com>Sent: Tue, 03 May 2016
19:21:47To: <gmx-us...@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
Respected Sir,
I am new user of gromacs. When I use the following command
gmx grompp -f ions.mdp -c 1aki_solv.gro -p topol.top -o ions.tpr
I get the following error :Number of coordinates in coordinate file does not
match topology file.
Please tell me how can I correct the number o