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

[Justin Lemkul]

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

-- 

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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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