[gmx-users] Complication of errors, .itp file regarding

[Justin Lemkul]

On 12/17/17 8:18 AM, RAHUL SURESH wrote:
> Dear all
>
> Let me put forth the thing first. I have generated the parameter file using
> fftk(structure.par) and derived the respective topology file(structure.top)
> using topotools of vmd. Now to get the itp fiule, I manually copied the
> necessary data from structure.top and made structure.itp file.
>
> For the command
> * "gmx grompp -f em.mdp -c solv.gro -p alz.top -o ions.tpr"*
>   I get so many warning and errors.
>
> WARNING 1 [file THC.itp, line 3]:
>    Overriding atomtype CG2D1
>
> WARNING 31 [file THC.itp, line 37]:
>    Overriding Bond parameters.
>
> WARNING 35 [file THC.itp, line 111]:
>    Overriding U-B parameters.
>
> *69 warning messages*
>
> ERROR 1 [file THC.itp, line 158]:
>    Encountered a second block of parameters for dihedral type 9 for the same
>    atoms, with either different parameters and/or the first block has
>    multiple lines. This is not supported.

The above errors are due to the fact that your molecule's .itp file 
includes parameters that are already part of the parent force field, 
hence grompp overrides them with the second instance. Don't do this. If 
an interaction is already specifically parametrized and is part of the 
force field, use it. Remove duplicated parameters from your .itp file.

> *47 error messages*
>
> and finally
>
>
>
>
>
> *Fatal error:number of coordinates in coordinate file (solv.gro,
> 31285)             does not match topology (alz.top, 31330)*
> Please make it simple.

The answer to this problem is always the same - incorrect bookkeeping. 
Check your work starting from addition of solvent and count how many of 
each species there are to make sure you've done things correctly.

-Justin

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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