It's just a regular peptide with the sequence KLVFFAE
One of the Phenylalanines (the first one from the left is replaced
with phenylglycine. The ends are capped with acetyl and NH2 groups. I
could parametrize the acetyl, because that needed me to put in just
one dihedral. There are 7 strands of the peptide which form a sheet.
Seven such sheets in turn are stacked on top of each other. This is
the system I want to do MD on. I did use -merge in the pdb2gmx
conversion.
Thanks
Ashutosh
On Mar 6, 2006, at 1:37 PM, Mark Abraham wrote:
Ashutosh Jogalekar wrote:
I am trying to do an MD on a peptide with an unnatural amino acid
residue. When I convert the pdb to the gro file and generate
the .top file, the amino acid residues are numbered incorrectly.
The first three are numbered ok from 1-3. But after the third
one, the next one is numbered 5 instead of 4, and after that, all
the others are numbered successively. Why is this happening?
We needed more information. Where is the unnatural amino acid? What
does your pdb file have in the region 3-5?
Mark
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