[gmx-users] Opening aminoacids.dat file during grommp

Mark Abraham Mark.Abraham at anu.edu.au
Tue Oct 13 15:59:46 CEST 2009

Lum Nforbi wrote:
> Hello all,
> I am running grommp which kind of goes "successfully" but I am a little 
> concerned about the fact that one of the messages in the terminal says 
> "opening aminoacids.dat file" and in another message says "OTHER: 2000 
> residues found." I guess this 2000 is refering to the  2000 water 
> molecules in my system since I am using just pure water and the command 
> line I am using is:
> grompp -f waters.mdp -c waters2000_b.gro -p waters2000.top -o 
> watersinput.tpr
>  I did not specify an amino acid file and I am not sure where that 
> statement "opening aminoacids.dat file" is coming from. Will this affect 
> my run?

That's normal - this file merely names residues that grompp should 
consider to be "protein". You have none, which doesn't matter.


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