[gmx-users] grompp question(caoch)

[David]

On Thu, 2004-05-20 at 09:16, コウ チ wrote:
> hi
>  i want to run a protein mdrun in a solvent cubic(minize_box.gro).With 
> minize_box.gro spc216.gro and spc.itp i have updated the target topology 
> file.but when i want to make a tpr file i got a error messarge. 
> fatal error : number of coordinates in coordinate file 
> (minimized_water.gro, 31372) 
>             does not match topology (aki.top, 0) 

grompp only finds 0 atoms in your topology, so something must be wrong
there.

>    i have checked the files tail of  minimized_water.gro is 
> 10144SOL     OW31364   0.096   5.638   5.754 
> 10144SOL    HW131365   0.131   5.597   5.670 
> 10144SOL    HW231366   0.006   5.600   5.774 
> 10145SOL     OW31367   0.044   6.039   6.277 
> 10145SOL    HW131368  -0.015   6.119   6.281 
> 10145SOL    HW231369   0.059   6.004   6.370 
> 10146SOL     OW31370   5.625   6.663   5.886 
> 10146SOL    HW131371   5.724   6.652   5.877 
> 10146SOL    HW231372   5.585   6.577   5.918 
>   6.84203   6.84203   6.84203 
> and head of aki.top is 
> ;       File 'aki.top' was generated 
> ;       By user: root (0) 
> ;       On host: localhost.localdomain 
> ;       At date: Sun May 16 11:59:13 2004 
> ; 
> ;       This is your topology file 
> ;       LYSOZYME 
> ; 
> ; Include forcefield parameters 
> #include "ffG43a1.itp" 
> 
> [ moleculetype ] 
> ; Name            nrexcl 
> Protein             3 
> 
> [ atoms ] 
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB  
>  chargeB      massB 
>     1         NL      1   LYSH      N      1      0.129    14.0067   ; qtot 
> 0.1 
> the tail of aki.top is 
> [ system ] 
> ; Name 
> LYSOZYME in water 
> 
> [ molecules ] 
> ; Compound        #mols 
> Protein             1 
> SOL                78 
> SOL              9939 
> 
> it seems the numbers in two files can not match. how can i deal with it?
> 
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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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