[gmx-users] Fw: Fatal error: Bonded/nonbonded atom type '1' not found

[Michal Kolinski]

----- Original Message ----- 
From: Michal Kolinski 
To: gmx-users at gromacs.org 
Sent: Tuesday, November 02, 2004 3:43 PM
Subject: Fw: Fatal error: Bonded/nonbonded atom type '1' not found



----- Original Message ----- 
From: Michal Kolinski 
To: gmx-users at gromacs.org 
Sent: Tuesday, November 02, 2004 3:05 PM
Subject: Fatal error: Bonded/nonbonded atom type '1' not found


Hi all.

I'm learning Gromacs.  I'm trying to run  EM for a small molecue - naltrexon in box filled with water.

I made topology file using PRODRG2 server.  When I try to run  grompp with 

 

grompp -v -f em -c gb.gro -o em -p naltrexwl.top 

 

command I get error:

..

..

..

  

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.8#

checking input for internal consistency...

calling /lib/cpp...

processing topology...

WARNING 1 [file "naltrexx.itp", line 1]:

  Incorrect number of atomtypes for dihedral (2 instead of 2 or 4)

Cleaning up temporary file gromppxYFxEe

Fatal error: Bonded/nonbonded atom type '1' not found

 

 

Maybe someone knows what the problem might be??!!  THANKS

 

My naltrexwl.top  file :

 

#include "ffgmx2.itp"

 

#include "naltrexx.itp"

 

 

#include "spc.itp"

 

[system]

naltrexx in water

 

[molecules]

 

naltrexx      1

SOL               144

 

My naltrexx.itp file  :

 

 

gnr   charge     mass

     1      CR61     1  MOL     C19     1    0.000  13.0190

     2      CR61     1  MOL     C18     1    0.000  13.0190

     3       CH2     1  MOL     C17     2    0.058  14.0270

     4        NL     1  MOL      N1     2   -0.316  14.0067

     5       CH2     1  MOL     C16     2    0.058  14.0270

     6       CH2     1  MOL     C15     2    0.059  14.0270

     7       CH1     1  MOL     C13     2    0.141  12.0110

     8        CB     1  MOL     C12     3    0.000  12.0110

     9        CB     1  MOL      C4     4    0.185  12.0110

    10        OS     1  MOL      O2     4   -0.132  15.9994

    11       CS1     1  MOL      C5     4    0.289  13.0190

    12        CB     1  MOL      C6     4    0.185  12.0110

    13         O     1  MOL      O3     4   -0.527  15.9994

    14       CH2     1  MOL      C7     5    0.049  14.0270

    15       CH2     1  MOL      C8     5    0.049  14.0270

    16       CH1     1  MOL     C14     5    0.119  12.0110

    17        OA     1  MOL      O4     5   -0.256  15.9994

    18        HO     1  MOL     HAB     5    0.039   1.0080

    19

    ...

    ...    

    ...

 

 

 

 

my gb.gro file :

 

PRODRG COORDS

  458

    1MOL    C19    1   0.443   1.362   0.826

    1MOL    C18    2   0.572   1.339   0.796

    1MOL    C17    3   0.618   1.225   0.709

  

  

    ...

    ...    

    ...



 

  145SOL     OW  456   1.352   0.041   0.168

  145SOL    HW1  457   1.387   0.000   0.084

  145SOL    HW2  458   1.262   0.003   0.188

   1.76800   1.87300   1.48700

 

 

 

thanks  for your help!
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