[gmx-users] Parameters for AOT molecule/Too few parameters on line

[Lum Nforbi]

Hello all,

    I have built a parameter file for the AOT surfactant molecule and tried
to minimize the energy of a mixture of several of this molecule and water
molecules but I have the warnings at the bottom part of this mail. Gromacs
basically goes through all the lines of parameters starting from [ bonds ]
and says the parameters are too few. I am also using the charmm force field.


    Here is the way I constructed the aot.itp parameter file. I am not sure
this is correct. Excerpts of the parameter file are belowl.

- I drew the AOT molecule and did the bond and angle connections in the
molecule.The atom names are provided by the ffcharmm27.atp file. All values
are obtained from the ffcharmmbon.itp file and ffcharmmnb.itp file.
- I am not sure how to build the dihedrals since the are X's in the [
dihedrals ] section of the ffcharmmbon.itp file.

My question is: Why does the program say I have few parameters while I just
out together parameters from the charmm27 force field? Please, if I am doing
something wrong, can someone let me know?
  [ bonds ]
; i    j    func    b0    kb
SL    O2L    1    0.1448    451872.0
SL      CTL1    1       0.1800  376560.0
CTL1    HAL1    1    0.1111    258571.2
[ angles ]
; i    j    k    func    th0    cth    ub0    cub
02L     SL      O2L     5       109.47    1087.84    0.245    29288.0
O2L     SL      CTL1    5       98.0    711.28    0.0    0.0
SL      CTL1    HAL1    5       110.10    288.696    0.2179    18853.104
[ dihedrals ]
; i    j    k    l    func    phi0    cp    mult
HAL1    CTL1    SL    O2L    9    0.00    0.0    3
CTL2    OSL    SL    O2L    9    0.00    0.0    3
CL    CTL1    SL    O2L    9    0.00    0.0    3
X    CTL1    CTL2    X    9    0.00    0.8368    3
X    CTL1    CTL2    X    9    0.00    0.8368    3
[ atoms ]
;name    at.num    mass    charge    ptype    sigma    epsilon
CL    6    12.01100    0.62    A    0.356359487256    0.29288
HAL1    1    1.008000    0.09    A    0.235197261589    0.092048
HAL2    1    1.008000    0.09    A    0.238760856462    0.117152
[ pairs ]
; i    j    func    sigma1-4    epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CTL1    CTL1    1    0.338541512893    0.04184
CTL1    CTL2    1    0.338541512893    0.04184
CTL1    CTL3    1    0.338541512893    0.04184

WARNING 141 [file aot_2.itp, line 228]:
  Too few parameters on line (source file toppush.c, line 1248)


WARNING 142 [file aot_2.itp, line 229]:
  Too few parameters on line (source file toppush.c, line 1248)

Excluding 3 bonded neighbours molecule type 'AOT'
Excluding 2 bonded neighbours molecule type 'SOL'

NOTE 1 [file aotwater.top, line 19]:
  System has non-zero total charge: -1.350000e+01

processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:    60      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Making dummy/rest group for T-Coupling containing 1110 elements
Making dummy/rest group for Acceleration containing 1110 elements
Making dummy/rest group for Freeze containing 1110 elements
Making dummy/rest group for Energy Mon. containing 1110 elements
Making dummy/rest group for VCM containing 1110 elements
Number of degrees of freedom in T-Coupling group rest is 3192.00
Making dummy/rest group for User1 containing 1110 elements
Making dummy/rest group for User2 containing 1110 elements
Making dummy/rest group for XTC containing 1110 elements
Making dummy/rest group for Or. Res. Fit containing 1110 elements
Making dummy/rest group for QMMM containing 1110 elements
T-Coupling       has 1 element(s): rest
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file aotwater_min.mdp, line unknown]:
  You are using a plain Coulomb cut-off, which might produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 1 Mb of data
writing run input file...

There were 2 notes

There were 142 warnings

-------------------------------------------------------
Program grompp, VERSION 4.0.5
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (142), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------


I appreciate your answers.

Lum
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