[gmx-users] Protein in water/DMSO mixture with Amber

[Simone Cirri]

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