[gmx-users] rtp file

Mark Abraham Mark.Abraham at anu.edu.au
Sun Apr 20 15:50:37 CEST 2008

shahrbanoo karbalaee wrote:
> hi
>  my peptide(13 aa), has a NH2 bond in C terminal.I must rtp file for 
> modified     amino acid   (phe -NH2).
> and another else that I dont know.please say to me what do i do if  i 
> want run md  with this peptide.?
> Do I need  to change hdb file  and amino acid .dat?.please help me.

The information you seem to be after is all in chapter 5 and/or 
http://wiki.gromacs.org/index.php/Parameterization. If you need to 
present pdb2gmx with a structure including a residue with an unnatural 
heavy atom then you will need to make a new .rtp file entry. However the 
above is not a topic for newcomers. It is highly recommended that you 
get some MD and/or GROMACS experience with some other system first - at 
the very least do all the tutorial material you can find.


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