[gmx-users] Membrane error

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 5 08:00:58 CEST 2006

Kushal Seth wrote:
> Dear All!
> Thanks for your replies.My CPP path seems to be ok as far as the 
> location is concerened and I continue to get the same error messsages.

The fact that you are receiving a cpp exit code (32512 in your email) 
means it is being found and run, so Sukit's suggestion isn't applicable 

> Is there any other reason for that ( my top files also seem to be 
> wroking for other simulations )

Reading the error message carefully will usually help you...

>      >     -------------------------------------------------------
>      >     Program grompp, VERSION 3.3
>      >     Source code file: grompp.c, line: 427
>      >
>      >     Fatal error:
>      >     number of coordinates in coordinate file
>      >     (binaryCR-Ochol-box-largeZ.pdb, 10280)
>      >                 does not match topology (mytop-nowater1.top, 0)

The absence of atoms in your .top file suggests that it is not being 
generated correctly, or is trying to include non-existent files. Have a 
look at it and try work out what is going wrong.


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