Hello. I am trying to create new parameters for a new acetylated
serine (acetylated on the sidechain OH). I've tried to follow some of
the previous instructions I got here on the mailing list. Here is a
brief excerpt from a previous answer I got:
I suggest you create a new amino acid: an actylated serine. Give it a
unique name and change the protein pdb file to reflect this name at the
appropriate serine (you should delete the hydroxyl hydrogen, also.)
You may have to remove the water to have room for the acetyl group
(but even then it may not fit.) You can just leave the atoms of the
serine (minus hydrogen), and leap will fill in the acetyl group with
geometry as specified by the new residue descriptor file (which can be
of various formats: mol2 file, .off library file, or prep file.)
There are two main approaches to new residue generation: antechamber and
RED. See postings in this mailing list for pointers. Several people
have posted about generating phosphorylated serine residues, for
example.
This suggestion helped me in 90% of the way. The problem is that the
sum of the charges in my new aminoacid is somewhat wrong. Here is what
I've been trying to do.
I've created a new residue by the name SAC. This is my serine residue
which contains my serine frame plus my acetyl group attached to the
sidechain OH (without the H obviously).
In order to calculate the partial charges of this residue, I had to
end-cap it with an NME and a ACE groups. These groups are there to
substitute the missing bonds I generated when I removed the residue
from the protein. So, what I actually submit for my RESP calculation
is a serine residue with an extra methyl group at my N and an extra
methyl group at my C terminus, plus my C=O(CH3) group attached to the
O of my former sidechain OH.
After I examine the resulting partial charges, I see that, once I
eliminate my endcaps, the total sum is -0.5454. This means that once I
rejoin my custom aminoacid with my protein, the total sum is -1.5454.
Something is wrong here and probably is by something I am doing wrong.
Some help here would really be appreciated.
Fabrício
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Received on Wed Sep 21 2011 - 06:00:12 PDT
