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

[RAHUL SURESH]

Dear all

I managed to overcome above errors by manually creating an .itp file from
the parameter file of ffTK. But i end up with 139 warnings stating




*"Too few parameters on line (source file
/home/viji/Downloads/Gromacs/gromacs-2016.4/src/gromacs/gmxpreprocess/toppush.cpp,
line 1841) "*
Going through previous threads, the error arise because I have used atom
type instead of numbers in bond and angle section of .itp file. To change
all the names to number is really a difficult task ( though not impossible
) and take lot ground work and much much time. I would like to know if
something can be done actually to create an itp through some script which
are already available, rather dumping all my time over this renumbering
process. Please sort out some better way.




On Mon, 18 Dec 2017 at 12:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==================================================
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*