[gmx-users] NO such a molecule type

[Mark Abraham]

Morteza Khabiri wrote:
> 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
> system.
> But after running grompp i faced with the following ERRORR:
> 
> calling cpp...
> topol.top:43944:18: error: Br.itp: No such file or directory

That really does mean what it says. Filenames are case-sensitive. cpp 
should look in your working directory, the directory(ies) of your -I 
flags and the directory contained in GMXLIB environment variable. It's 
conceivable that you have a broken cpp if you haven't known it to work 
correctly before - e.g. it might not look in the working directory by 
default. Try in your .mdp file "define = -DFLEXIBLE -I."

Mark

> 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?
> 
> thanks
> 
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