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

Anna Marabotti anna.marabotti at isa.cnr.it
Thu May 21 16:33:35 CEST 2009

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
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
"If you think you are too small to make a difference, try sleeping with a mosquito"

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