[gmx-users] number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093)

[Mark Abraham]

I've no idea what the real limitation in InflateGRO might be, but if it is
based on the [moleculetype], then a combined protein+ligand [moleculetype]
might be effectlve.

Mark


On Sat, Apr 13, 2013 at 2:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On Sat, Apr 13, 2013 at 4:57 AM, swati rana <swati.rana088 at gmail.com>
> wrote:
>
> > Hi,
> >
> > I am facing this issue with the energy minimization. The following is the
> > output when i try to pack the lipids around the protein:
> >
> > Steepest Descents:
> >    Tolerance (Fmax)   =  1.00000e+01
> >    Number of steps    =        20000
> > Step=   14, Dmax= 1.2e-06 nm, Epot=  3.37981e+20 Fmax=         inf, atom=
> > 147
> > Energy minimization has stopped, but the forces havenot converged to the
> > requested precision Fmax < 10 (whichmay not be possible for your system).
> > It
> > stoppedbecause the algorithm tried to make a new step whose sizewas too
> > small, or there was no change in the energy sincelast step. Either way,
> we
> > regard the minimization asconverged to within the available machine
> > precision,given your starting configuration and EM parameters.
> >
> > i know this is not an error but the potential energy is very high i went
> > through the mailing list as well but could not get the answer for my
> > question.
> >
> > THERE IS AN OVERLAP IN POPC AND LIGAND. WHEN I SELECT MY LIGAND IN PYMOL
> > simultaneously ONE POPC ATOM ALSO GETS SELECTED and i understand that is
> > the problem but what should be done to correct this. i tried to
> reposition
> > the ligand and copied its coordinates in the last that worked in
> system.gro
> > file but again when system_inflated.gro file was generated again there
> was
> > an overlap. please tell how to solve this issue. how to correct this
> > overlap thing. Do i have to number each atom from the start to end in a
> > flow like instead of popc 1st molecule to be numbered as 1 should i
> > renumber it to what was the last for proteins.
> >
> >
> I don't know if InflateGRO is even capable of dealing with ligands. Try the
> workflow without it to make sure it works for a simple system of protein
> and lipids. Then try again with the ligand included. If the latter fails,
> then it's simply a limitation in InflateGRO. In that case, you'll have to
> build the protein-lipid system completely and then figure out some way to
> insert the ligand. Numbering should not be an issue at all; positions are
> the problem here.
>
> -Justin
>
> --
>
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540)
> 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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