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.
Mark
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