[gmx-users] Coordinate file does not match topology

[Sheyore Omovie]

Thanks,
But this is my first real simulation, So I'll appreciate it if you can tell 
me how to determine the number of ions to add with genion.
Thanks
John


>From: Alan Dodd <anoddlad at yahoo.com>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Subject: Re: [gmx-users] Coordinate file does not match topology
>Date: Thu, 7 Jun 2007 23:26:01 -0700 (PDT)
>
>Small errors like that are usually down to things like running genion and 
>not changing the .top.  I think I made a problem for myself once with 
>non-consecutive atom numbering, too.
>
>----- Original Message ----
>From: Mark Abraham <Mark.Abraham at anu.edu.au>
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Sent: Friday, June 8, 2007 3:48:28 AM
>Subject: Re: [gmx-users] Coordinate file does not match topology
>
>
>Sheyore Omovie wrote:
> > Dear gromacs users,
> > While trying to preprocess my files with grompp, i got the ff error
> > message:
> > "Number of coordinates in coordinate file (b4em.gro, 2312) does not
> > match topology (twopolypeptide.top, 2291)"
> > How can I fix this?
>
>Make them match. Assuming you haven't managed a gross mismatch of files,
>your [molecules] section of your .top probably isn't right. Chapter five
>of the manual is your friend here.
>
>Mark
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