[gmx-users] Re: Ndx for Enzyme-peptide inhibitor
Jorge Hernanez Fernandez
jorgehf at cbi.cnptia.embrapa.br
Thu Feb 5 15:33:00 CET 2004
First, thanks for your ansuer. Let me explain more detailed....
> Message: 7
> Date: Wed, 04 Feb 2004 17:19:01 +0100
> From: Anton Feenstra <feenstra at chem.vu.nl>
> Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Re: gmx-users digest, Vol 1 #1248 - 7 msgs
> Reply-To: gmx-users at gromacs.org
> Jorge Hernanez Fernandez wrote:
> > Dear GMXers!:
> > Im using GMX for a year, and actually interested in the free energy
> > evaluation in a Enzyme-inhibitor system. My protein is a metallo (Zn) and
> > inhibitor is a small peptide.
> > The central problem is that pdb2gmx read my system as a one whole
> > protein, and am not able to create a working index to obtain my peptide as a
> > separate Ener-group. Make_ndx is working find (I think
> For temperature coupling, all atoms must be in *one* group only. I'm
> not sure from your descxription what your system looks like, exactly,
> but I'd suggest you couple enzyme-zn-inhibitor to one, and solvent
> (water and sodium) to another bath. For that, you will only need to
> combine groups 1 and 12 (protein + Zn), and 13 and 14 (Sol and Na).
> and chenge the t-coupl line in your mdp file accordingly.
Separate T-coupl for each group works fine for a 1.5 ps MD, and is
important to me maintain it .... The problem is the evaluation of the Energy
interactions in Enzyme-inhibitor system. Although inhibitor is properly
defined in index.ndx (and without Zn!!!), pdb2gmx works with "Protein", and
grompp halt with an "dual Zn position in 0 group (System) and 14 group
Part of my file.mdp:
; Berendsen temperature coupling is off in two groups
Tcoupl = berendsen
tc-grps = Protein Zn BDK SOL Na
tau_t = 0.1 0.1 0.1 0.1 0.1
ref_t = 312 312 312 312 312
; Energy monitoring
energygrps = Protein Zn BDK SOL
I'm missing something important?? What I m doing wrong??
Thanks a lot for your time:
== Dr. JORGE HERNANDEZ FERNANDEZ ==
===== Lab. de Biofisica e Bioquimica =====
===== CAT-CEPID - Instituto Butantan =====
====== Ave Vital Brasil, 1500 S.P. ======
==== S.B.I.- EMBRAPA - BioInformatica ====
C.p. 6041 Cidade Universitária "Zeferino Vaz"
===== Barão Geraldo Campinas S.P. ======
=========== 13080-970 ==============
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