[gmx-users] Large system

[Bratin Kumar Das]

Check the .itp files...it's possible that you forgot to delete atom number
from the last of the file

On Wed 2 Jan, 2019, 12:18 PM Anuj Ray <anujray107 at gmail.com wrote:

> Sir,
>
> Since the array size of .gro/.pdb file for atom number is not greater than
> 5 digits, that's why if my system has >= 100000 atoms then, it shows that
> no. of coordinates mismatch in .gro and .top file. Although the file
> corrected_wat_DMPC_18_32.pdb has 153216 coordinates, i get the following
> error.
>
> Command line:
>   gmx grompp -f minim.mdp -c corrected_wat_DMPC_18_32.pdb -p dmpctopol.top
> -o em.tpr
>
> Fatal error:
> number of coordinates in coordinate file (corrected_wat_DMPC_18_32.pdb,
> 99999)
>              does not match topology (dmpctopol.top, 153216)
>
>
>
>
>
>
>
>
> On Wed, Jan 2, 2019 at 12:18 AM <pbuscemi at q.com> wrote:
>
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> >
> > As suggested,  compare the number of molecules/atoms implied in your top
> > file against that in your gro/pdb file.  This is one aspect of Gromacs
> that
> > it never gets wrong.
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se
> > <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of Bratin
> > Kumar Das
> > Sent: Tuesday, January 01, 2019 5:22 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Large system
> >
> > There must be something wrong in your pdb or gro file. Give the proper
> > error
> > message. They way you told your problem..no one can understand.
> >
> > On 01-Jan-2019 11:41 AM, "Anuj Ray" <anujray107 at gmail.com> wrote:
> >
> > Respected Sir
> >
> > I am trying to prepare a minimization input file (.tpr) for a system
> having
> > 153216 atoms but the grompp command is reading only upto 99999 atoms.
> What
> > is the procedure to prepare the input for such system?
> >
> > Regards
> > Anuj
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