[gmx-users] number of coordinates in coordinate file (system_inflated.gro, 9331) number of coordinates in coordinate file does not match topology

[Terry]

On Tue, Feb 15, 2011 at 5:25 PM, Parul tew <parultew at gmail.com> wrote:

> Hi all,
> first I would like to thank Justin A. Lemkul for the tutorials provided which are very helpful for new users like me.
> I am doing a membrane protein simulation and now doing packing of the lipids around the protein. I had run the inflategro.pl script and
>
> and now I am facing a problem doing energy minimization of my inflated system (contatining protein and the lipid membrane) using grompp.
> I have updated my topology file accordingly ie removed the spc.itp, ions.itp it now only contains protein and dppc
>
> the protein is of 3881 atoms but after updating my topolgy it still gives the following error:
> Fatal error:
> number of coordinates in coordinate file (system_inflated.gro, 9331)
>              does not match topology (topol.top, 10281)
>
> As i understand it could be because of the deleted lipids of the system, if so how can I know the deleted number of lipids.
>
> My topology file looks like
> -----------------------------------------------------------------------------------------------------------------------------
>
> ;
> ;	This is your topology file
> ;	protein
> ;
> ; Include forcefield parameters
> #include "ffG53a6_lipid.itp"
>
> [ moleculetype ]
> ; Name            nrexcl
> Protein_A           3
>
> [ atoms ]
> .
> .
> .
> .
> ; Strong position restraints for InflateGRO
> #ifdef STRONG_POSRES
> #include "strong_posre.itp"
> #endif
>
> ; Include DPPC chain topology
> #include "dppc.itp"
>
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
>
> [ system ]
> ; Name
> protein
> 128-Lipid DPPC Bilayer
>
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> DPPC                128
>
>
After insertion, there are probably several DPPC molecules removed. Check
outputs from inflategro.pl, then update accordingly.

Terry

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> thank you,
> Parul Tewatia
>
>
>
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