[gmx-users] errors position restraints in a linux cluster

[David]

On Fri, 2004-10-01 at 00:23, gerph at correo.unam.mx wrote:
> Dear David,
> I verified my PBS script, you are right I interchange the extention of my inputs
>   by misstake, but with the correct inputs I get the same warnings. I check the
> topology and coordinates carefully finding that some Na are sorted in diferent
> positions of the sequence in the coordinates,  
> amino acid
> H20 (n+1)
> Na 
> Na
> H20
> H20
> Na
> Na
> H20
> .
> .
> .
> Na
> Na
> Na
> 
If this is the order in the coordinate file you need the same order in
the top file:
Protein 1
sol     n+1
na      2
sol     m
na      x
sol    y

> I found an easy way to follow working (not elegant), run all proccess in my
> linux workstation before position restrain and then export the files to the
> cluster. 
> 
> I am confused by the errors, could you explain to me. 
> 
> Thanks,
> 
> Gerardo Perez Hernandez 
> 
> -------------------------------------------------
> www.correo.unam.mx
> UNAMonos Comunicándonos
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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