[gmx-users] Protein in water/DMSO mixture with Amber
Simone Cirri
simonecirri at gmail.com
Fri Apr 16 12:00:19 CEST 2010
Hi all,
to say the truth I already sent a message regarding this subject some
months ago, but since so much time has passed I thought I'd open a new
thread, also because the situation has quite evolved.
I'm trying to set up a simulation of a small (62 residues) protein in
a mixture of water and DMSO with the AMBER99 forcefield. I found the
parameters for such forcefield in the literature and used them to
build a dmso.itp. Following yuor previous suggestions, I also obtained
a dmso.gro file downloading a .sdf file from Pubchem and converting it
to a .pdb and eventually to a .gro.
Then I followed the mini-tutorial in the Gromacs site on simulations
of mixed solvents: I added some DMSO molecules with genbox -ci -nmol
and then filled the box with TIP3P water molecules. I also added 9 Cl-
ions and, judging from what I could see with a visualization program,
everything was fine.
The problem came when I tried to run the energy minimization. I got the error:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 100
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
after only 5 minimization steps. I searched in the GROMACS site and in
this mailing list as well to find out what the error meant and I read
that this error can be sometimes ignored if the potential energy of
the system is already low enough to run the simulation... but my Epot
is 7.6367096e+16 . To be completely sure, I tried to run an MD
simulation, but it immediately crashed with a "water molecule cannot
be settled" error, which does not surprise me.
What did I do wrong? Do I have to assume that there is something wrong
in my dmso.itp file or in the way I ran the minimization?
Thank you very much; I'm pasting my dmso.itp and em.mdp here.
###DMSO.ITP###
[ moleculetype ]
; molname nrexcl
DMSO 2
[ atoms ]
#ifdef _FF_AMBER99
; nr type resnr residue atom cgnr charge mass
1 amber99_47 1 DMSO S 1 0.3155 32.06000 ;
amber S type
2 amber99_41 1 DMSO O 1 -0.5205 16.00000 ;
amber O type
3 amber99_11 1 DMSO CT1 1 -0.3244 12.01000 ;
amber C type
4 amber99_19 1 DMSO HT11 1 0.1423 1.00800
; amber H type
5 amber99_19 1 DMSO HT12 1 0.1423
1.00800 ; amber H type
6 amber99_19 1 DMSO HT13 1 0.1423
1.00800 ; amber H type
7 amber99_11 1 DMSO CT2 1 -0.3244
12.01000 ; amber C type
8 amber99_19 1 DMSO HT21 1 0.1423 1.00800
; amber H type
9 amber99_19 1 DMSO HT22 1 0.1423
1.00800 ; amber H type
10 amber99_19 1 DMSO HT23 1 0.1423
1.00800 ; amber H type
#endif
[ bonds ]
; ai aj funct b0 kb
1 2 1 0.153 238602
1 3 1 0.181 95022
3 4 1 0.109 142324
3 5 1 0.109 142324
3 6 1 0.109 142324
1 7 1 0.181 95022
7 8 1 0.109 142324
7 9 1 0.109 142324
7 10 1 0.109 142324
[ angles ]
; ai aj ak funct theta kt
3 1 2 1 106.75 334.88
3 1 7 1 97.40 259.53
2 1 7 1 106.75 334.88
4 3 1 1 109.50 209.30
6 3 1 1 109.50 209.30
5 3 1 1 109.50 209.30
5 3 4 1 109.50 146.51
5 3 6 1 109.50 146.51
4 3 6 1 109.50 146.51
9 7 10 1 109.50 146.51
8 7 9 1 109.50 146.51
8 7 10 1 109.50 146.51
9 7 1 1 109.50 209.30
10 7 1 1 109.50 209.30
8 7 1 1 109.50 209.30
[ dihedrals ]
; ai aj ak al funct xi kxi pn
2 1 3 6 1 180 3.558 2
2 1 3 4 1 180 3.558 2
2 1 3 5 1 180 3.558 2
2 1 7 8 1 180 3.558 2
2 1 7 9 1 180 3.558 2
2 1 7 10 1 180 3.558 2
3 1 7 8 1 180 3.558 2
3 1 7 9 1 180 3.558 2
3 1 7 10 1 180 3.558 2
7 1 3 4 1 180 3.558 2
7 1 3 5 1 180 3.558 2
7 1 3 6 1 180 3.558 2
###EM.MDP###
title = 1HAA
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
dt = 0.002 ; ps !
nsteps = 10000
nstlist = 10
ns_type = grid
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
pme_order = 6
ewald_rtol = 1e-5
optimize_fft = yes
;
; Energy minimizing stuff
;
emtol = 100.0
emstep = 0.00001
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