[gmx-users] nonbonded molecules and atoms

[Justin Lemkul]

On 10/6/16 10:51 PM, sumair ahmed wrote:
>   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.
>

This topology is completely out of order, a mix of force field directives and 
molecule directives.  Spend some time in Chapter 5 of the manual.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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