[gmx-users] in vacuo minimization of a multimeric protein

[Anna Marabotti]

Dear Justin,
thank you very much for suggestion. Now it works!
Anna

Message: 4
Date: Thu, 21 May 2009 10:39:33 -0400
From: "Justin A. Lemkul" <jalemkul at vt.edu>
Subject: Re: [gmx-users] in vacuo minimization of a multimeric protein
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <4A1567A5.5070806 at vt.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Anna Marabotti wrote:
> Dear gmx-users,
> I'm trying to do a mild minimization on a homohexameric protein in vacuo. I used the following options in
the
> em.mdp file:
> 
> title               =  mild-mini
> cpp                 =  /usr/bin/cpp        
> define              =  -DFLEXIBLE 
> constraints         =  none
> integrator          =  steep
> nsteps              =  500
> emtol               =  5000
> emstep              =  0.1
> nstcomm             =  1
> ns_type             =  grid
> nstlist             =  5
> rlist               =  0.9
> coulombtype         =  PME
> rcoulomb            =  0.9
> rvdw                =  1.4
> fourierspacing      =  0.12 
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order           =  4 
> ewald_rtol          =  1e-5
> optimize_fft        =  yes
> 
> I simply converted my protein from .pdb format to .gro using pdb2gmx, and then I submitted immediately to
> minimization, since I only would like to relieve some eventual steric clashes between subunits, without
> proceed with a further MD simulation and without distorting too much the protein structure.
> At the end of the run I found that the 6 subunits of my protein (which are not covalently linked to each
> others) are separated in two dimers and two monomers. I tried also the minimization in water, although for
> this system I don't want water, but the result is not changing: the protein separates in subunits. The same
if
> I apply PBC (the first time I applied it, then I saw that the subunits separated, I check the gmx-users list
> and delete pbc from the em.mdp, but the results are quite the same). I also changed ns_type to simple,
without
> success. Have you got any suggestion? Thanks in advance

If you have gone straight from pdb2gmx to grompp, then your box size is likely 
inappropriate.  Use editconf -c -d to define a suitably large box.

-Justin

> Anna
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
> ____________________________________________________
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