[gmx-users] [Fwd: TFE 33%]

chiradip chatterjee chiradip75 at yahoo.co.uk
Sun Feb 18 01:03:16 CET 2007

Specify exact number of TFE and Water present in your
*.pdb file to *.top file..also specify *.itp of TFE in
the top file...


--- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:

> > i've been dealing with a simple simulation
> > using a TFE & SPC for my solvent box but i stopped
> every time at the
> > (steep or em.mdp) stuff all the time. It send me
> this message: number of
> > coordinates in coordinate file does not match
> topology ( xxxx.pdb, top
> > 0) !!!! what should i do to over this step? do i
> need to change xxxx.top
> > file whith something? or the error backs to the
> steep or em.mdp stuff?
> > Thanks
> Please describe your problem fully... "at the (steep
> or em.mdp) stuff" 
> doesn't help anybody work out your problem, and
> makes them not want to 
> help you. When you want free help, you have to work
> at making it easy 
> for someone to give it to you. If you're paying
> them, then do whatever 
> you like :-)
> Nonetheless, it is clear that you have made an error
> with the formatting 
> of your .top file. Read chapter 5 carefully and then
> see where your .top 
> file doesn't satisfy the format described.
> Alternatively, start again 
> with a .top file that does work for just water, and
> work in the TFE again.
> Mark
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Chiradip Chatterjee 
Post Doctoral Research Associate 
Department of Chemistry and Biochemistry 
University of California, Santa Barabara 
Mobile :1-805-637-7995
E-mail:chiradip75 at yahoo.co.uk 
       cchatterjee at chem.ucsb.edu 
Home Page: www.chem.ucsb.edu/~cchatterjee/ 
Group home page : www.chem.ucsb.edu/~gerig/

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