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

[SeungPyo Hong]

Christopher,

I am a novice in this field and have the same experience like you.
I hope this will help you:

1. Have you compared the molecule's name in topology file in [ molecules ]
section and molecules's name in .itp file?
2. Does residue names in the topology file match with the name in coordinate
file?
If not, it is better to math them.

3. Or, rewrite .mpd file with Linux editor.
I don't know much about Linux. But when I rewrite .mpd file again it works.

Seungpyo Hong

On 7/24/07, Moore, Jonathan (J) <JMoore2 at dow.com> wrote:
>
>  Christopher,
>
> I'm afraid I don't have any other ideas.  To confirm if your editing
> method is OK, I would run a GROMACS example with an undmodified .mdp file
> and then modify it (making some trivial change) by your method and see if it
> still runs OK.
>
> Jonathan
>
> ____________________________
> *Jonathan Moore, Ph.D.*
> Research and Engineering Sciences - New Products
> Core R&D
> The Dow Chemical Company
> 1702 Building, Office 300E
> Midland, MI 48674  USA
> Phone:  (989) 636-9765
> Fax: (989) 636-4019
> E Mail: jmoore2 at dow.com
>
>
>  ------------------------------
> *From:* gmx-users-bounces at gromacs.org [mailto:
> gmx-users-bounces at gromacs.org] *On Behalf Of *Christopher Stiles
> *Sent:* Monday, July 23, 2007 4:42 PM
> *To:* gmx-users at gromacs.org
> *Subject:* Re: Re: [gmx-users] number of coordinates in coordinate file
> does not match topology
>
>  Jonathan,
>
>         I had originally done that but I read through the archives and found out that that was an issue. To solve this issue I used the following command in Vim: "set ff=unix" and then I wrote it. So I do not believe that it is an issue any longer as I mentioned on the walk through of my steps at http://cs86.com/CNSE/SWNT.htm.
>
>
>
> Do you have any other ideas on why this might be happening? If so please let me know, and thank you for your help so far!
>
>
>
> Also please let me know if that command in vim would solve the problem.
>
>
>
> ~Christopher Stiles
>
> College of Nanoscale Science and Engineering (CNSE)
>
> State University of New York, Albany, New York 12203, USA
>
>
>
> >
>
> >Christopher,
>
> >
>
> >When I've had this problem before (# of coordinates in coordinate file does not match topology (0)), it has been because >I edited the mdp file under Windows (mismatch between Windows and unix end-of-line characters).  Is it possible that you >have done the same?  If so, try to run your mdp thr
>  ough the dos2unix utility.
>
> >
>
> >
>
> >Jonathan
>
> >
>
> >____________________________
>
> >Jonathan Moore, Ph.D.
>
> >Research and Engineering Sciences - New Products
>
> >Core R&D <
>  /SPAN>
>
> >The Dow Chemical Company
>
> >1702 Building, Office 300E
>
> >Midland, MI 48674  USA
>
> >Phone:  (989) 636-9765
>
> >Fax: (989) 636-4019
>
> >E Mail: jm
>  oore2 at dow.com <http://www.gromacs.org/mailman/listinfo/gmx-users>
>
> >
>
> >
>
> >
>
> >
>
> >  _____
>
> >
>
> >>From: gmx-users-bounces at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users> [mailto:gmx-users-bounces at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>] On Behalf Of Christopher Stiles
>
> >>Sent: Monday, July 23, 2007 12:08 PM
>
> >>To: gmx-users at gromacs.org <http://www.gromacs.org/mailman/listinfo/gmx-users>
>
> >>Subject: Re: [gmx-users] number of coordinates in coordinate file does not match topology
>
> >>
>
> >>
>
> >>
>
> >>I have already asked about this but I think maybe I did not give enough information so I made the following page:
>
> >>
>
> >>http://cs86.com/CNSE/SWNT.htm
>
> >>It outlines every step I have taken and where I am stuck is at the end with grompp when it spits out the following >>error:
>
> >>
>
> >>********************************************************************************************************<
>  /o:p>
>
> >>
>
> >>Fatal error:
>
> >>
>
> >>number of coordinates in coordinate file (SWNT_6_6_144_b4em.gro, 699)
>
> >>
>
> >>             does not match topology (SWNT_6_6_144.top, 0)
>
> >>
>
> >> also it updates the SWNT_6_6_144.top file to: SWNT_6_6_144.top
>
> >>********************************************************************************************************
>
> >>I have looked through both the *.gro and *.top files and I can not find anything wrong with them; maybe one of you will >>have better luck.
>
> >>
>
> >>Any help or advice is greatly appreciated!
>
> >>
>
> >>
>
> >>
>
> >>~Christopher Stiles
>
> >>College of Nanoscale Science and Engineering (CNSE)
>
> >>State University of New York, Albany, New York 12203, USA
>
> >>
>
>
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