[gmx-users] NO such a molecule type

Morteza Khabiri khabiri at greentech.cz
Sat Nov 15 18:15:26 CET 2008

Dear gmx users

I want to run the system by OPLS forcefield. My system has protein, water
and  1 ligand (Boromohexane) and NA. At the first I put the protein in the
water and minimized it then add the ligand to system. I already made a itp
file for the ligand. I add the ligand itp file to the topology file which
was include the itp file of protein and water and Na to nautral the
But after running grompp i faced with the following ERRORR:

calling cpp...
topol.top:43944:18: error: Br.itp: No such file or directory
cpp exit code: 256
Tried to execute: 'cpp  -I/usr/local/gromacs/share/top -DFLEXIBLE
topol.top > grompp4OawMo'
The 'cpp' command is defined in the .mdp file
processing topology...
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 11433
Excluding 1 bonded neighbours for NA+ 18
Cleaning up temporary file grompp4OawMo

Program grompp, VERSION 3.3.3
Source code file: toppush.c, line: 1396

Fatal error:
No such moleculetype MOL

As you see it says that Br.itp file does not exist in this directory which
is not true. All of my files are in the same folder and I am confusing
what should be wrong?


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