[gmx-users] nonbonded molecules and atoms

[sumair ahmed]

  Dear all,
I am new to gromacs software. I was trying to make simple sodium nitrate (NaNO3) molecules. I have made .pdb file. then I got .gro file from pdb2gmx. But, I got struck in .itp file. Please help me. ( Na is nonbonded to any of N and O in NaNO3. And Na is also nonbonded to Na of 2nd NaNO3 molecule and so on). I have taken 50 NaNO3 molecules. Given below is .itp file, I cannot progress through grompp. as it is showing error as syntax error at '1    2    yes    1.0    1.0'. If possible correct my .itp file.

[ defaults ]
;nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
1    2    yes    1.0    1.0

[ moleculetype ]
; molname   nrexcl
NaN         4

[ atomtypes ]
;name    atnum    mass        charge    ptype    sigma        epsilon
Na    11    22.98977    1.000    A    3.33045e-01    1.15980e-02
O    8    15.99940    -0.598    A    2.86000e-01    8.78640e-01
O    8    15.99940    -0.598    A    2.86000e-01    8.78640e-01
O    8    15.99940    -0.598    A    2.86000e-01    8.78640e-01
N    7    14.00670    0.794    A    3.15000e-01    7.11280e-01

[ nonbond_params ]
;i    j    func    sigma        epsilonNa    Na  1    3.33045e-01    3.33045e-01 Na    O    1    3.33045e-01    1.15980e-02
Na    N    1    3.33045e-01    1.15980e-02

[ constraints ]
; ai    aj    funct    b0

[exclusions ]
1    2
1    3
1    4
1    5

Waiting for kind reply,Thank you, With Regards, SUMAIR FAISAL AHMED.