[gmx-users] gramicidin A

Mark Abraham Mark.Abraham at anu.edu.au
Sat Nov 3 09:23:32 CET 2007

pragya chohan wrote:
> hi 
> I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. 

D-amino acids are enantiomers of L-amino acids. Thus they're 
topologically identical. So you can use the same topology for them, 
unless your force field has an interaction that varies with chirality. 
You know already whether your force field has one of them, right? If it 
doesn't, then you can just change some names.

> I generated .itp from prodrg server and included the above stated things in .rtp file. But again when i ran pdb2gmx i got the same error..
> Residue 'DLE' not found in residue topology database.


You need to do some more work in understanding the purpose of running 
pdb2gmx, the way of using an .itp file, and/or understanding the .rtp 
file syntax. Check out http://wiki.gromacs.org/index.php/topology_file 
and chapter 5 of the GROMACS manual.


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