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

[Anna Marabotti]

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
______________________________________________
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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