[gmx-users] number of coordinates in coordinate file does not match topology

[Justin A. Lemkul]

Quoting shikha agarwal <shikhaiiitabi at gmail.com>:

> hello
>
>
> I m unable to update the [ molecules ] directive of topol_pope.top .
>
> grompp -f minim.mdp -c system_inflated.gro -p topol_pope.top -o em1.tpr
>
>
> Fatal error:
> number of coordinates in coordinate file (system_inflated.gro, 20782)
>              does not match topology (topol_pope.top, 37867)
>
>
>
> this is my .top file
> ; Include chain topologies
> #include "forcefield.itp"
> #include "pope.itp"
>
> ; Include water topology
> #include "spc.itp"
>
> ; Include ion topologies
> #include "ions.itp"
>
> ; System specifications
> [ system ]
> 340-Lipid POPE Bilayer
>
> [ molecules ]
> ; molecule name nr.
> POPE 340
> SOL 6729
>
> this is system.gro
>
> Gnomes, ROck Monsters And Chili Sauce
>  41229
>
> this is sytem_inflated.gro
>
> What you read here has nothing to do with anything. So you don't have to
> read it. Thank you.
> 20782
>
> but there is 3362 protein atom and 17680 lipid in sytem_inflated.gro then
> why  inflategro.pl script is generating wrong total count .
>
>

It isn't wrong. Inflategro deletes all water molecules and any lipids that
overlap with the protein. You need to update the number of lipid molecules in
your topology accordingly. There is also no reference to a protein in your
topology. It appears to contain only lipid information, so you're doing
something very wrong here.

-Justin

>
> help!
> thank for ur support !
>
> with regards :
>
> shikha
>


========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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