On 12/7/12 10:41 AM, James Starlight wrote:
Today I've tried to simulate complexes of my protein with the cyclic
GMP parametrized by ATB's. (below the recent parametrisation for
charges of that molecule done by am1 algorithm)

[ moleculetype ]
; Name   nrexcl
_N4P     3
[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
     1    NT    1    _N4P     N2    1   -0.848  14.0067
     2     H    1    _N4P    H22    1    0.424   1.0080
     3     H    1    _N4P    H21    1    0.424   1.0080      ;  0.000
     4    NR    1    _N4P     N1    2   -0.684  14.0067
     5     H    1    _N4P     H1    2    0.437   1.0080
     6     C    1    _N4P     C2    2    0.779  12.0110
     7    NR    1    _N4P     N3    2   -0.678  14.0067
     8     C    1    _N4P     C4    2    0.440  12.0110
     9    NR    1    _N4P     N9    2   -0.294  14.0067      ;  0.000
    10     C    1    _N4P     C8    3    0.272  12.0110
    11    HC    1    _N4P    H01    3    0.141   1.0080
    12     O    1    _N4P     O6    3   -0.555  15.9994
    13     C    1    _N4P     C6    3    0.608  12.0110
    14     C    1    _N4P     C5    3    0.101  12.0110
    15    NR    1    _N4P     N7    3   -0.567  14.0067      ;  0.000
    16    OE    1    _N4P    O4*    4   -0.451  15.9994
    17   CH1    1    _N4P    C1*    4    0.451  13.0190      ;  0.000
    18    OA    1    _N4P    O5*    5   -0.394  15.9994
    19     P    1    _N4P    PAQ    5    0.974  30.9738
    20    OM    1    _N4P    OAR    5   -0.616  15.9994
    21    OA    1    _N4P    O3*    5   -0.390  15.9994
    22    OA    1    _N4P    OAS    5   -0.584  15.9994
    23     H    1    _N4P    H03    5    0.491   1.0080
    24   CH2    1    _N4P    C5*    5    0.281  14.0270
    25   CH1    1    _N4P    C4*    5    0.238  13.0190      ;  0.000
    26   CH1    1    _N4P    C3*    6    0.000  13.0190      ;  0.000
    27   CH1    1    _N4P    C2*    7    0.181  13.0190
    28    OA    1    _N4P    O2*    7   -0.645  15.9994
    29     H    1    _N4P    H8M    7    0.464   1.0080      ;  0.000

In all cases my system have always been crushed after equilibration
run ( during that phase with the posres applied on both protein as
well as ligand the system was stabile) with the errors like

Step 19, time 0.038 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 1.203662, max 11.750027 (between atoms 4289 and 4287)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
    4288   4287   89.5    0.2277   1.1291      0.1000
    4292   4287   90.5    0.1304   0.9898      0.1350
    4289   4287   90.4    0.1056   1.2750      0.1000
    4318   4303   30.8    0.1531   0.1816      0.1530
    4304   4303   45.2    0.1097   0.1531      0.1090
    4309   4310   90.0    0.2629   0.3419      0.1000
    4299   4290   84.2    0.1404   0.1641      0.1400
    4292   4290   89.4    0.1362   0.5025      0.1380
    4291   4290   89.2    0.1563   0.2142      0.1000
    4293   4292   89.1    0.1252   0.5682      0.1320
    4294   4293   78.1    0.1387   0.3906      0.1350
    4300   4294   92.2    0.1385   0.4639      0.1390
    4295   4294   91.1    0.1365   0.5711      0.1380
    4303   4295   43.4    0.1482   0.1954      0.1470
    4296   4295   36.6    0.1408   0.1593      0.1400
    4301   4296   89.9    0.1323   0.5162      0.1320
    4297   4296   32.5    0.1089   0.1343      0.1090
    4299   4298   87.0    0.1230   0.2758      0.1230
    4300   4299   89.8    0.1431   0.5922      0.1430
    4301   4300   79.0    0.1381   0.1928      0.1380


Fatal error:
1 particles communicated to PME node 26 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension y.
This usually means that your system is not well equilibrated.
For more information and tips for troubleshooting, please check the GROMACS

After that my system have been crashed and than produced many
step*.pdb files in the work dirr.

It's intresting that with the prodrg topology of that mollecule ( with
worst charge distribution) I've never such problems. Might that error
be due to the wrong geometry parametrisation (e.g incorect dihedrals)
of the cGMP made by ATB ?


Simulate all components of your system separately and follow http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System. Dihedrals should not be a major issue, since all of them can be adequately described by those already present in the parent force field. Check against DGUA.

-Justin

--
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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