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

[RAHUL SURESH]

On Mon, 18 Dec 2017 at 1:27 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/17/17 2:54 PM, RAHUL SURESH wrote:
> > 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.
> >
>
> Sounds like you have a totally broken topology. Solve the first issue
> you posted and to which I responded; it's much simpler to deal with.


Dear Justin

I got the first issue solved and this is what I get now. Broken topology..?
I have actually manually written it.  Is there any other option to generate
the itp file from parameter file of ffTK?



>
> -Justin
>
> >
> >
> > 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
> >>
> >> ==================================================
> >>
> >> --
> >> Gromacs Users mailing list
> >>
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>
> --
> ==================================================
>
> 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
>
> ==================================================
>
> --
> Gromacs Users mailing list
>
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-- 
*Regards,*
*Rahul Suresh*
*Research Scholar*
*Bharathiar University*
*Coimbatore*