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: amarabo...@isa.cnr.it
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
____________________________________________________
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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