[gmx-users] grompp error!

Thu Dec 29 15:16:19 CET 2005

Maybe you should check the time label and size of your topology files to select the correct .top file. Something works well in linux does not apply to windows--are you using the MS Windows port of Gromacs?

In your mail:
>From: Rahul Karyappa <r.karyappa at ncl.res.in>
>Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>To: gmx-users at gromacs.org
>Subject: [gmx-users] grompp error!
>Date:Thu, 29 Dec 2005 19:00:44 +0530 (IST)
>
>Dear all,
>
>   This is my topology file. When I run grompp command it gives me following error :
>
>Fatal error: number of coordinates in coordinate file (out.gro, 7048)does not match topology (topol1.top, 0).
>
>
>My .top file is as follows:
>
>Please help me out. Thanking you in advance.
>
>
>Rahul Karyappa
>
>
>
>; forcefield parameters
>
>[ defaults ]
>
>; nbfunc       
>comb-rule      
>gen-pairs       fudgeLJ fudgeQQ
>
>1              
>1              
>no             
>1.0     1.0
>
>
>[ atomtypes ]
>
>;name       
>mass      charge  
>ptype           
>c6           c12
>
>   OM   
>15.99940     
>-0.736       A  
>0.22617E-02   0.74158E-06
>
>    S   
>32.06000     
>+1.751       A  
>0.99844E-02   0.13078E-04
>
>   OS   
>15.99940     
>-0.736       A  
>0.22617E-02   0.74158E-06
>
>   HC    
>1.00800      
>0.000       A  
>0.0           0.0
>
>   C2   
>12.01100      
>0.000       A  
>0.90975E-02   0.35333E-04
>
>   C3   
>12.01100      
>0.000       A  
>0.88765E-02   0.26150E-04
>
>   OW   
>15.99940     
>-0.820       A  
>0.26171E-02   0.26331E-05
>
>   HW    
>1.00800      
>0.410       A  
>0.00000E+00   0.00000E+00
>
>   Na   
>22.98980     
>+1.000       A  
>0.72059E-04   0.21014E-07
>
>  CR6   
>12.01100      
>0.000       A  
>0.55132E-02   0.15120E-04
>
>   Mg   
>24.3050      
>+1.100       A  
>0.72059E-04   0.21014E-07
>
>  OY1    15.99940     
>-0.550       A  
>0.26171E-02   0.26331E-05
>
>  OY2    15.99940     
>-0.550       A  
>0.26171E-02   0.26331E-05
>
>  OY3    15.99940     
>-0.550       A  
>0.26171E-02   0.26331E-05
>
>  OY4    15.99940     
>-0.758       A  
>0.26171E-02   0.26331E-05
>
>  OY5    15.99940     
>-0.758       A  
>0.26171E-02   0.26331E-05
>
>  OY6    15.99940     
>-0.792       A  
>0.26171E-02   0.26331E-05
>
>  OY7    15.99940     
>-0.867       A  
>0.26171E-02   0.26331E-05
>
>  OY8    15.99940     
>-0.867       A  
>0.26171E-02   0.26331E-05
>
>  OY9    15.99940     
>-0.683       A  
>0.26171E-02   0.26331E-05
>
>  AL1   
>26.9815      
>+1.450       A  
>0.72059E-04   0.21014E-07
>
>  SI1   
>28.0855      
>+1.100       A  
>0.72059E-04   0.21014E-07
>
>  SI2   
>28.0855      
>+1.100       A  
>0.72059E-04   0.21014E-07
>
>   H1    
>1.00800      
>0.200       A  
>0.0           0.0
>
>   
>
>
>[ nonbond_params ]
>
>  ; i    j
>func         
>c6           c12
>
>   OM   OW    1 0.24329E-02   0.29873E-05
>
>   OM   Na    1 0.40370E-03   0.44478E-06
>
>   OS   Na    1 0.40370E-03   0.17791E-06
>
>   OW   OS    1 0.24329E-02   0.19915E-05
>
>  CR6  CR6    1 0.0           0.0
>
>
>[ pairtypes ]
>
>  ; i    j
>func        
>cs6          cs12
>
>   OM   C2    1 0.32685E-02   0.22969E-05
>
>   OM   OS    1 0.22617E-02   0.74158E-06
>
>   OM    S    1 0.47520E-02   0.31143E-05
>
>   C2    S    1 0.68675E-02   0.96461E-05
>
>   C2   OS    1 0.32685E-02   0.22969E-05
>
>   C2   C2    1 0.47236E-02   0.71145E-05
>
>   C2   C3    1 0.56894E-02   0.92642E-05
>
>; Added manually
>
>   HC   C2    1         0.0  0.0
>
>   HC   C3    1         0.0  0.0
>
>   HC   OS    1         0.0  0.0
>
>   HC   S     1         0.0  0.0
>
>   HC   OM    1         0.0  0.0
>
>
>[ bondtypes ]
>
>  ; i    j
>func       
>b0          kb
>
>    S   OM    1   0.15000     376560.
>
>    S   OS    1   0.15000     376560.
>
>   OS   C2    1   0.14300     251040.
>
>   C2   C2    1   0.15300     334720.
>
>   C3   C2    1   0.15300     334720.
>
>   C2   HC    1   0.10900     292880.
>
>   C3   HC    1   0.10900     292880.
>
>  CR6  CR6    1   0.14120     600000.
>
>
>[ angletypes ]
>
>  ; i    j    k
>func      
>tHC         cth
>
>   OM    S   OM    1   109.500     500.080
>
>   OM    S   OS    1   109.500     500.080
>
>    S   OS   C2    1   120.000     397.480
>
>   OS   C2   C2    1   107.900     460.240
>
>   C2   C2   C2    1   111.000     460.240
>
>   C2   C2   C3    1   111.000     460.240
>
>   HC   C2   HC    1   109.500     292.880
>
>   C2   C2   HC    1   109.500     292.880
>
>   C3   C2   HC    1   109.500     292.880
>
>   C2   C3   HC    1   109.500     292.880
>
>   OS   C2   HC    1   109.500     292.880
>
>   HC   C3   HC    1   109.500     292.880
>
>
>[ dihedraltypes ]
>
>  ; i    l
>func       
>q0          cq
>
>    S   OS   
>1     0.000      
>3.766      3
>
>   OS   C2   
>1     0.000      
>3.766      3
>
>   C2   C2   
>1     0.000      
>5.858      3
>
>   C2   C3   
>1     0.000      
>5.858      3
>
>
>
>[ dihedraltypes ]
>
> C2  C2  3   9.2789   12.156  -13.120 -3.0597 26.240 -31.495
>
>
>
>
>
>
>; Include various molecular topologies
>
>#include "1unk.itp"
>
>#include "spc.itp"
>
>#include "1sds.itp"
>
>
>[ system ]
>
>; Name
>
>unk in water
>
>
>[ molecules ]
>
>; Compound        #mols
>
>unk              1
>
>Na            16
>
>SOL              2148
>
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