[gmx-users] .itp file error

[Justin Lemkul]

On 10/10/16 3:15 AM, sumair ahmed wrote:
> Dear user,
> After correcting many things in .itp file, still I am finding error as "1    1    yes    1.0    1.0". Can you please .itp file.
> [ defaults ]
> ;nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
> 1    1    yes    1.0    1.0
>
> [ 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        epsilon
> Na      Na    1    3.33045e-01    1.15980e-02
> Na        O    1    3.33045e-01    1.15980e-02
> Na        N    1    3.33045e-01    1.15980e-02
>
> [ moleculetype ]
> ; molname   nrexcl
> NaN         4
>
> [ constraints ]
> ; ai    aj    funct    b0
>   1    2    2    0.16000
>   1    3    2    0.16000
>   1    4    2    0.16000
>   1    5    2    0.16000
>
> [ exclusions ]
> 1    2
> 1    3
> 1    4
> 1    5
> 2    1
> 3    1
> 4    1
> 5    1I 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. N and O are bonded atoms). I have taken 50 NaNO3 molecules. If possible correct my .itp file. With Regards, SUMAIR FAISAL AHMED.
>

Please provide the full, exact error message.  Probably you have something wrong 
with the way the .top #includes this .itp such that you're re-defining a 
[defaults] directive, but only the actual error message will tell us.

Also, you have no [atoms] defined, so there's no way that any [constraints], 
[exclusions], etc. can possibly make sense.  Spend some time in Chapter 5 of the 
manual, where the hierarchy is explained and example topologies are shown.

-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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