[gmx-users] Re: Ndx for Enzyme-peptide inhibitor

[Jorge Hernanez Fernandez]

Dear Anton:

      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.
> 
> -- 
> Groetjes,
> 
> Anton

       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
(inhibitor)" error.

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:
                                     Jorge H.F.
-- 
== Dr. JORGE HERNANDEZ FERNANDEZ ==

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